title: Liver sinusoidal endothelial cells constitute a major route for hemoglobin clearance

city: Warsaw

first: Michal

last: Mikula

address: Roentgena 5

department: Experimental Oncology

country: Poland

institute: Maria Skłodowska-Curie National Research Institute of Oncology

summary: Hemolysis of senescent erythrocytes occurs in the spleen, resulting in hemoglobin (Hb) release. Several diseases are associated with an increased risk of erythrocyte rupture. Iron recycling from Hb and Hb detoxification have been attributed to the sequestration of Hb-haptoglobin complexes by macrophages, however, other routes of Hb clearance might exist. We identified liver sinusoidal endothelial cells (LSECs) as the major cell type that sequesters Hb. Hb uptake involves macropinocytosis and is independent of haptoglobin and the Hb-haptoglobin receptor CD163. LSECs expressed heme oxygenase 1 and hepcidin-controlled ferroportin and were the most efficient cellular scavengers of Hb at doses below the haptoglobin binding capacity. Erythrocyte transfusion assays demonstrated that while splenic red pulp macrophages are efficient in erytrophagocytosis, liver Kupffer cells and LSECs are primarily involved in the clearance of erythrocyte ghosts and Hb, respectively. Using time-course injections of high doses of Hb in mice, we detected transient hepatic iron retention, early induction of Hmox1 specifically in LSECs, and elevation of ferroportin levels. This was associated with transcriptional activation of LSEC Bmp6, followed by hepcidin-mediated transient hypoferremia. Injection of Hb and iron-citrate elicited distinct transcriptional signatures in LSECs and the early Bmp6 induction was phenocopied by erythrocyte lysis upon phenylhydrazine. Collectively, we propose that LSECs provide a key mechanism for Hb clearance, a function that establishes the spleen-liver axis for physiological iron recycling from Hb and contributes to heme detoxification during hemolysis, coupled with the induction of the BMP6-hepcidin axis that restores homeostasis.

overall_design: We analyzed in total 4 versus 4 RNA samples derived from FACS-sorted LSECs obtained from young female Balb/c mouse mice, intravenously injected with PBS or free hemoglobin (10 mg), respectively.

first: Gabriela

last: Zurawska

first: Zuzanna

last: Sas

first: Aneta

last: Jończy

first: Patryk

last: Slusarczyk

first: Raghunandan

last: Mahadeva

first: Marta

last: Chwałek

first: Izabela

last: Rumieńczyk

first: Maria

last: Kulecka

first: Kamil

last: Jastrzębski

first: Michał

first: Anders

last: Etzerodt

last: Miączyńska

first: Tomasz

last: Rygiel

first: Katarzyna

last: Mleczko-Sanecka


title: Single Cell Multiomics Across Nine Mammals Reveals Cell Type Specific Regulatory Conservation in the Brain.

status: Public on Aug 06 2025

city: Huntsville

first: J.

middle: Nicholas

last: Cochran

state: AL

address: 601 Genome Way

country: USA

institute: HudsonAlpha Institute for Biotechnology

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

sample_organism:
Danio rerio
Homo sapiens
Felis catus
Equus caballus
Bos taurus
Oryctolagus cuniculus
Rattus norvegicus

overall_design: Refer to individual Series


title: Massively Parallel Screens Reveal Factors Influencing the Activity of a Diversity-Generating Retroelement Reconstituted in Escherichia coli [Tn-Seq]

city: Beverly

first: Hoong Chuin

last: Lim

state: MA

address: 44 Dunham Ridge Road

institute: New England Biolabs

summary: Some phages and microbes employ Diversity-Generating Retroelements (DGRs) to achieve rapid targeted adaptation. DGRs mutagenize a specific gene without harming the rest of the genome. Mutagenesis relies on the DGR reverse transcriptase (dRT), which is highly error-prone when transcribing adenines of an RNA template. The resulting mutagenized cDNA then alters the target gene through a poorly understood mechanism. Transplanting DGRs into a tractable organism, like Escherichia coli, holds promise for creating a powerful system for gene-targeted editing. Here, we successfully reconstituted the archetypal BPP DGR in E. coli, demonstrating that DGRs are "plug-and-play" systems adaptable to non-native hosts. Systematic analysis of reconstituted DGR established principles for target mutagenesis. Our results revealed that cytosine misincorporation is the most common error when dRT transcribes adenines. However, error rates peak in 5'-AAC-3' and 5'-ACC-3' contexts, driven by elevated adenine and guanosine misincorporations, respectively. Using high-throughput genetics, we discovered that cells lacking the single-stranded DNA exonuclease ExoI exhibit 15-fold higher DGR activity. Our evidence indicates that ExoI inhibits DGRs by binding a limited cellular factor, rather than through direct cDNA degradation. Finally, by profiling DGR targets across thousands of chromosomal loci, we discovered that DGRs preferentially edit targets near the replication origin and oriented in the same direction as replication. We showed that the directionality of replication underlies this bias, possibly through unwinding the target to facilitate base-pairing with incoming cDNA. These findings establish a reconstituted DGR system in E. coli and provide a foundation for optimizing targeted gene-editing applications in the future.

overall_design: Transposon sequencing data of a transposon that carried a DGR reporter to identify how genomic location and orientation affect DGR retrohoming. Transposon library sequenced before and after selection by DGR specific reporter. Reporter represents a defective kanamycin resistance gene and DGR targeting sequences transposed all over the genome.

first: Irem

last: Unlu

first: Marina

middle: K

last: Smiley

first: Vladimir

last: Potapov

first: Yoan

last: Renoux-Martin

first: Zhi-Yi

last: Sun


title: Myeloid cell states determine reinstatement of original immune environments in recurrent ovarian cancer

status: Public on Aug 01 2025

city: Lausanne

first: Aspram

last: Minasyan

address: Bugnon 25A

country: Switzerland

institute: Ludwig Institute for Cancer Research / CHUV

summary: Immunotherapy has produced disappointing results in recurrent ovarian cancer (OC). However, the prognostic value of tumour-infiltrating lymphocytes (TILs) is grounded on the analysis of treatment-naive tumours. To understand the immunobiology of recurrent cancers, and their evolution, we profiled 170 patient-matched primary-recurrent OC samples from 69 patients of two independent cohorts. By capturing heterogeneous TIL distributions, we identified four immune phenotypes associated with differential prognosis, TILs states and TILs:myeloid networks, which dictate malignant evolution after chemotherapy and recurrence. Notably, recurrent tumours recapitulate the immunogenic patterns of original cancers. Mirroring inflamed human OC, preclinical recurrent Brca1mut tumours maintained activated TILs:dendritic cells (DCs) niches and immunostimulatory tumour-associated macrophages (TAMs). Conversely, recurrent Brca1wt tumours displayed loss of TILs:DCs niches and accumulated immunosuppressive myeloid networks featuring Trem2/ApoEhigh TAMs and Nduf4l2high/Galectin3high malignant states. Our study highlights that persistent immunogenicity in recurrent OC is governed by the crosstalk between dissimilar myeloid cells and TILs, which is BRCA-dependent.

overall_design:
scRNA-seq of mouse ovarian cancer models: Trp53-/- Brca1-/- (hereby referred as Brca1mut) or Trp53-/- Brca1+/+ (or Brca1wt). We characterized solid tumors at baseline (referred as primary tumors) and relapse after chemotherapy treatment (referred as recurrent tumors). Therefore, the experiment included 4 arms and the single-cell samples belonging to each arm are assigned below:

Brca1wt primary: group BRCA-A (mice A1-A5 and A_pooled) and group BRCA-B (mice B7-B10 and B_pooled).

Brca1wt recurrent: group BRCAP1 (mice P1_3, P1_13, and P1_pooled) and group BRCAP2 (mice P2_1, P2_47, and P2_pooled).

Brca1mut primary: group BRCA-C (mice C11-C15 and C_pooled) and group BRCA-D (mice D16-D20 and D_pooled).

Brca1mut recurrent: group BRCAB1 (mice B1_21, B1_23, and B1_pooled) and group BRCAB2 (mice B2_28, B2_29, and B2_pooled).

Note: This represents a multiplexed sc RNAseq assay (see methods). Most cells were successfully de-multiplexed to individual mice. Unassigned cells from each group of the corresponding experimental arm were grouped as additional "pooled" sc samples.

first: Eleonora

last: Ghisoni

first: Alizée

middle: J

last: Grimm

first: Noémie

last: Fahr

first: Mathieu

last: Desbuisson

first: Denarda

last: Dangaj


title: DHT-AR regulation in LNCaP cells and HOXC9 stably expressed LNCaP cells

status: Public on Jul 31 2025

city: Kaga, Itabashi-ku

first: Takao

last: Susa

state: Tokyo

country: Japan

institute: Teikyo University, School of Mediocine

summary: To analyze the regulatory mechanism of DHT in LNCaP cells (WT) and HOXC9 stably expressed LNCaP cells (C9), we analyzed the effects of 10-7M of DHT on LNCaP cells.

overall_design: The number of samples analyzed was 4 (N=1). Each cells were treated with vehicle (V) or 10-7M of DHT, respectively.


title: DHT-AR and D3-VDR regulation in LNCaP cells

summary: To analyze the regulatory mechanism of DHT and D3 via their respective nuclear receptors in LNCaP cells, we analyzed the effects of those hormones on LNCaP cells when they were treated with siRNA for their respective nuclear receptors.

overall_design: The number of samples analyzed was 9 (N=1). Control siRNA (siCT) and mixture of siRNA for the AR (siAR)and VDR (siVDR) were transfected into LNCaP cells. Each siRNA transfected cells were treated with vehicle (V), 10-7M of DHT or 10-7M of 1,25(OH)2D3 (D3), respectively.


title: Restoring Taxane Efficacy in Castration Resistant Prostate Cancer Through Targeting Menin

city: Istanbul

first: Hamzah

last: Syed

address: Rumelifeneri Yolu

department: School of Medicine

country: Turkey

institute: Koç University

summary: Prostate cancer (PC) typically depends on hormones for growth, with androgen deprivation therapy (ADT) serving as the primary treatment. However, many patients progress to a castration-resistant (CR) stage, where their tumor becomes unresponsive to ADT. Despite the common use of conventional chemotherapeutics like taxanes (docetaxel, cabazitaxel), the majority of patients experience recurrence. To uncover the mechanisms underlying the drug-resistant phenotype, we developed docetaxel-resistant CRPC cell lines, and  through a drug library screen, we identified MLL-Menin and MLL-WDR5 inhibitors that overcome taxane resistance and significantly induced G2/M arrest and apoptosis. To determine the roles of individual proteins in the MLL complexes, we silenced several MLL partner proteins , and the absence of Menin and LEDGF particularly halted the growth of the resistant cells while showing no significant effect on parentals. Notably, parental cells with Menin silencing failed to develop resistance even after prolonged exposure, unlike their Menin-expressing counterparts, highlighting the critical role of Menin in the resistance process. Menin knockouts were analyzed through RNA-sequencing, and several gene sets, including E2F targets, G2/M checkpoints, and mTORC1 pathways, were found to be negatively regulated in taxane-resistant cells. The ablation of Menin led to a reduction in mTOR levels, and ChIP-qPCR analysis confirmed that Menin was enriched on the mTOR promoter. According to TCGA clinical data, the correlation between MEN1 and mTOR became stronger as the disease advanced to metastatic stages. Furthermore, the combination of the mTOR inhibitor Torin1 and docetaxel enhanced the sensitivity of our resistant cells. Menin deficiency reduced cell proliferation and key expression of cell cycle genes (Cyclin D1, CDK20). Rescue experiments reversed these effects, and Menin showed significant enrichment of the Cyclin D1 and CDK20 promoters. Finally, Menin loss impaired docetaxel resistant CRPC growth in our in vivo model. Our data demonstrate the essentiality of Menin for docetaxel resistance and suggest a combined approach targeting both Menin and mTOR to improve taxane therapy responses. Additionally, Menin regulates some key cell cycle genes to promote the G1/S transition, emphasizing its critical role in cell cycle regulation and the growth of taxane-resistant CRPC.

overall_design: To understand the molecular mechanisms underlying Menin-mediated inhibition in taxane-resistant CRPC, we aimed to analyze the transcriptome of Du145-P and Du145-DtxR cells following Menin knockout.  We conducted gene expression profiling using RNA-seq data from both non-target guided and Menin-guided Du145-P and Du145-DtxR cells.

first: Ipek

last: Bulut

first: Buse

last: Cevatemre

first: Neslihan

last: Yuksel-Catal

first: Tamer

middle: T

last: Onder

first: Ceyda

last: Acilan


title: Toxin-antitoxin deletions in Legionella pneumophila reveal unusual cell death and contact-dependent survival responses during genotoxic stress [Lp_cipro_RNAseq]

city: Toronto

first: Alexander

last: Ensminger

state: Ontario

address: 661 University Avenue

country: Canada

institute: University of Toronto

summary: Bacteria must contend with near constant environmental stresses, and to tolerate these cellular assaults, have evolved numerous stress response pathways and programs. One such strategy is the adoption of a dormant state, whereby cells restrict their growth and await a reversion to favourable conditions. A notable example of this is the formation of persister cells, which are a quiescent subpopulation that display increased tolerance to antibiotic killing. The genetics of persistence remain poorly understood, however bacterial genes called toxin-antitoxin (TA) systems have long been implicated in the persistence phenotype. TA systems are abundant genetic elements in bacteria that can function as growth toggling molecular switches, yet their role in persister formation is highly controversial. To address this, we constructed a pan-TA deletion strain (∆7TA) of the bacterial pathogen Legionella pneumophila to examine how a strain devoid of these genes tolerates cellular stress. We identified a single putative TA system (Lpg1604-05) that is activated specifically in response to genotoxic stress, however this system leads to cell death during stress rather than promoting survival. In the absence of Lpg1604-05, cells do not die during stress exposure and instead adopt a viable but non-culturable state. Strikingly, while persister survival during DNA stress is dramatically improved when Lpg1604-05 is deleted, this enhanced survival can be conferred to wild-type cells in a contact-dependent manner during co-culture with the deletion strain. This is dependent, however, on a sufficient proportion of the mixed population being deletion mutants. Despite having homology only to other TA systems, Lpg1604-05 displays non-canonical activity and we hypothesize that it has undergone exaptation, leading to integration into the cell’s stress response pathway and conservation within L. pneumophila’s core genome. Overall, our work demonstrates the stress-specific activation of a putative TA system and its involvement in facilitating cell death, rather than survival, during stressful conditions. These findings reveal both a new physiological function for TA systems in bacteria, as well as a heretofore undescribed phenomenon of contact-dependent survival within persister cells. This expands the functional scope of an omnipresent class of bacterial genes and suggests that domestication of mobilome genes may be an overlooked source of de novo genetic circuitry.

overall_design: These samples consist of wild-type (WT) Legionella pneumophila (LP) and a strain with a single TA system (lpg1604-05; DEL16) deleted from its genome. Both strains were treated with genotoxic stress using the antibiotic ciprofloxacin to compare how their transcriptomes changed during stress exposure. Prior to stress exposure (T0), 1 hr of stress exposure (T1), and 6 hr of stress exposure (T2) were the time points when RNA was extracted for bulk sequencing. There are two biological replicates for each strain + time point.

first: Jordan

last: Lin

first: Alex


title: Micro-C reveals MORC/ApiAP2-mediated links between distant, functionally related genes in the human malaria parasite

city: Parul

first: Parul

last: Singh

address: 25-28, rue du Docteur Roux

country: France

institute: Institut Pasteur

summary: Genome organization plays a significant role in silencing heterochromatinized genes in the most virulent human malaria parasite, Plasmodium falciparum. However, it remains unclear how heterochromatinized genes spatially cluster or if active genes are also organized in a specific manner. We used Micro-C to achieve a near-nucleosome resolution DNA-DNA contact map, which revealed new inter- and intrachromosomal heterochromatic and euchromatic structures in the blood stage parasite. We observed subtelomeric fold structures that facilitate interactions amongst heterochromatinized genes involved in antigenic variation. In addition, we identified long-range intra- and interchromosomal interactions amongst active, stage-specific genes. Both structures are mediated by AP2-P, an ApiAP2 transcription factor, and a putative MORC chromatin remodeler, and functional specificity is achieved via combinatorial binding with other sequence-specific DNA-binding factors. This study provides unprecedented insight into the organizational machinery used by this medically important eukaryotic parasite to spatially coordinate genes underlying antigenic variation and to co-activate stage-specific genes.

sample_organism:
Plasmodium falciparum
Plasmodium falciparum NF54
Plasmodium falciparum 3D7

overall_design:
MicroC experiment was performed on Wild type, Control and AP2-P knockdown samples to investigate the DNA-DNA interactions.
MicroC experiment was performed on Wild type samples to investigate the DNA-DNA interactions.

first: Jacques

last: Serizay

first: Justine

last: Couble

first: Sebastian

last: Baumgarten

first: Jessica

middle: M

last: Bryant


title: Toxin-antitoxin deletions in Legionella pneumophila reveal unusual cell death and contact-dependent survival responses during genotoxic stress [Lp_growth_phase_RNAseq]

overall_design: These samples consist of wild-type (WT) Legionella pneumophila (LP) and a strain with a single TA system (lpg1604-05; DEL) deleted from its genome. Both strains were grown to two different growth phases to compare how their transcriptomes changed during stress exposure. Early exponential growth (OD1) and late exponential growth (OD3) were the time points when RNA was extracted for bulk sequencing. There are two biological replicates for each strain + growth phase.


title: Bacterial type II topoisomerases cleave DNA in a species-specific manner

status: Public on Jul 30 2025

city: Bethesda

first: Ian

middle: L

last: Morgan

state: MD

address: 50 Center Dr.

institute: National Heart Lung and Blood Institute

summary: The type II topoisomerases, gyrase and topoisomerase IV, are essential enzymes in nearly all bacteria and are the targets of fluoroquinolones, which are some of the most widely prescribed broad-spectrum antibacterials in clinical use. As part of their catalytic cycle, gyrase and topoisomerase IV transiently cleave DNA in a sequence-dependent manner. However, it is unclear whether this sequence-dependence is species-specific. Therefore, using our recently developed SHAN-seq method, we mapped and compared cleavage sites for type II topoisomerases from three different pathogenic bacterial species, Escherichia coli, Bacillus anthracis, and Mycobacterium tuberculosis in the presence of the fluoroquinolone, ciprofloxacin. We found that the enzymes have substantially different DNA cleavage specificities that vary between gyrase and topoisomerase IV, across species, with supercoil chirality, and in response to ciprofloxacin. Our results demonstrate that bacterial species fine-tune the DNA cleavage specificity of their type II topoisomerases. This finding suggests that cleavage specificity may play important physiological roles and, in turn, may affect the susceptibility of bacteria to fluoroquinolone antibacterials.

overall_design: Supercoiled pBR322 DNA was cleaved with DNA gyrase or topoisomerase IV and spiked with three DNA oligonucleotides. The DNA was subject to standard DNA-seq library preparation to label the enzyme-cleaved ends, fragmented, and subject to a second round of standard DNA-seq library preparation to label the fragmented ends. The labelled DNA was pair-end sequenced and mapped to the plasmid and spike-in oligonucleotide reference sequences. The reads from the topo-cleaved plasmid DNA ends were normalized by the reads from the spike-in ends and were used to determine the gyrase or topo IV cleavage levels at each position on the plasmid.

first: Jeffrey

last: Jian

first: Jillian

middle: F

last: Armenia

first: Neil

last: Osheroff

first: Keir

middle: C

last: Neuman


title: Benchmarking of Computational Demultiplexing Methods for Single-Nucleus RNA Sequencing Data [dataset 1]

city: Leuven

first: Hywel

middle: Llewelyn

last: Roderick

address: Gasthuisberg

department: Cardiovascular Sciences

country: Belgium

institute: KULeuven

summary: Single-nucleus RNA sequencing enables high-resolution profiling of complex tissues, but its high cost limits large-scale studies. Sample pooling with genetic demultiplexing is a scalable solution, yet comparative benchmarks are lacking. We benchmarked four widely used tools using variants from SNP arrays or extracted from matched bulk RNA-Seq. Performance, including accuracy, runtime, robustness, and scalability, was evaluated. Real-world application to 10x RNA-Seq from human and multi-species heart tissue demonstrates the tools' utility for demultiplexing and doublet removal.

overall_design: Six matching RNA-seq of the individual snRNA-seq experiments used for the simulated datasets

first: Yile

last: Fu

first: Mohamad

last: Youness

first: Alessia

last: Virzì

first: Xinran

last: Song

first: Michiel

middle: R

last: Tubeeckx

first: Gilles

middle: W

last: De Keulenaer

first: Hein

last: Heidbuchel

first: Vincent

last: Segers

first: Karin

last: Sipido

first: Bernard

last: Thienpont

first: H


title: Benchmarking of Computational Demultiplexing Methods for Single-Nucleus RNA Sequencing Data [dataset 2]

sample_organism:
Homo sapiens
Ovis aries

platform_organism:
Homo sapiens
Ovis aries

overall_design: snRNA-seq was applied to: 1) six patients for the simulated dataset (sequenced by 1-sample-per-lane); 2) four patients for the real-world dataset (sequenced by 2-sample-per-lane); 3) four patients for the application dataset (sequenced by 4-sample-per-lane); 4) 2 samples for the species-mixed dataset (1 human, 1 sheep).


title: The Mechanism Study of Intermittent Fasting in Glioblastoma Suppression via Gut Microbiota-mediated m6A Modification

city: Guangxi

first: Jun

last: Meng

address: ShuangYong Road

country: China

institute: Guangxi Medical University

summary: Glioblastoma Multiforme (GBM) is one of the most malignant tumors, characterized by high treatment costs and poor outcomes, thus urgently necessitating the development of new therapeutic approaches. Recent studies have found that intermittent fasting (IF) not only can suppress GBM among various tumors but also can reconstruct the gut microbiome and alter metabolism. However, the mechanism by which IF inhibits GBM is not yet fully understood. Using animal models, I discovered that IF can effectively suppress GBM and alter the gut microbiome. Furthermore, microbial metabolites such as methionine, m6A, and the m6A-targeted oncogene TGFB2 were also downregulated. Therefore, we hypothesize that IF, by reconstructing the gut microbiome, reduces the levels of microbial metabolite methionine, subsequently decreasing m6A in GBM, leading to the downregulation of the m6A-targeted oncogene TGFB2, thereby inhibiting the development of GBM.

overall_design: Lentivirus was used to induce a mouse glioblastoma model, and then the mice were subjected to intermittent fasting treatment and different experimental interventions on the basis of this treatment.

first: Yao

last: Lin

first: Xiaopeng

last: Hu

first: Zheng

last: Li

first: Dandan

last: Xiong

first: Yueqi

first: Xinyue

last: Xu

first: Hubin

last: Chen

first: Yi

last: Bao

first: Ziyi

last: Liu

first: Shuaiyi

last: Liang

first: Jiemei

last: Chu

first: Xuena

first: Xianning

last: Zhang

first: Sanqi

last: An


title: Genome accessibility profile at single cell level for conventional dendritic cells in human metastatic melanoma samples [snATAC-Seq]

city: Piscataway

first: Jiekun

last: Yang

state: NJ

address: 145 Bevier Rd

institute: Rutgers University

summary: Conventional dendritic cells (cDCs) has been shown to mediate immune checkpoint inhibitor responses in cancer patients. We used single nucleus ATAC sequencing (snATAC-seq) to analyze the epigenome of heterogeneous cDCs obtained from 14 human metastatic melanoma samples.

overall_design: We enzymatically digested and dissociated fresh tumor samples and analyzed using snATAC-seq.

first: Genevieve

last: Boland

first: Manolis

last: Kellis


title: Global Chromatin Remodeling and Widespread Differential Methylation Changes Underlie Brown Adipose Dysfunction and Dysregulated Metabolism in Response to Chronic Air Pollution Exposure: A Key Role for Reciprocal Regulation by HDAC9 and KDN2b

city: Baltimore

first: Bongsoo

last: Park

state: Maryland

address: 251 Bayview Blvd

department: Translational Gerontology Branch

institute: National Institute on Aging

type: Methylation profiling by high throughput sequencing

summary: The Global Burden of Disease implicates air pollution in mediating as much as 20% of Type 2 Diabetes mellitus globally. This profound impact of air pollution is supported by experimental studies suggesting effects on whole body metabolism and insulin resistance. We explored the effect of chronic inhalational air pollution exposure for 12 weeks, using a whole body inhalation device in mice that allows for daily exposure to concentrated ambient particulate matter <2.5 microns (6 hours/day, 5 days a week) on whole body metabolism and brown adipose tissue (BAT) function, with detailed investigation of differentially methylated regions (DMRs), chromatin accessibility (differential accessible regions or DARs), and differential gene expression (DEGs) levels using a combination of whole genome bisulfite sequencing, ATAC-sequencing, and RNA-sequencing respectively. A significant impact of chronic PM2.5 exposure on BAT function and whole-body metabolism through alterations in key BAT transcriptional programs resulting in increased redox stress, lipid deposition, fibrosis and reduced thermogenic function of BAT was observed. Significant differential methylation with evidence for both hypomethylation and hypermethylation involving target regions corresponding to both circadian and Nrf2 target genes including sites enriched for transcription factor binding sites implicated in redox stress, insulin resistance and BAT function in response to PM2.5. ATAC sequencing revealed widespread chromatin remodeling involving intronic regions and enhancer elements and loss of DARs in Ucp1 and Gclc major regulatory genes associated with thermogenesis and glutathione synthesis. DARs-DEGs interaction analysis pointed to functional pathways linked to diabetes development, fatty acid biosynthesis activation and activation of JAK-STAT, and MAPK in PM-exposed mice. Integrated analysis of DARs, DEGs and DMRs uncovered the Histone de-acetylase Hdac9 and Kdm2b, a Histone demethylase that demethylates 'Lys-4' and 'Lys-36' of histone H3. ChiP studies demonstrated that Hdac9 physically interacts with the BAT transcription factor Prdm16 and rorα in BAT decreasing their expression and providing at least one direct mechanism for our observations. Collectively our results results link DNA methylation with control of chromatin accessibility and gene expression changes involved in the alteration of brown fat metabolism linking chronic air pollution exposure with alterations in BAT and whole-body metabolism

overall_design: WGBS and ATAC-seq were performed to compare the epigenome of air pollution exposed mice and control mice

first: Palanivel

last: Rangasamy

first: Jean

middle: E

last: Dazard

first: Sanjay

last: Rajagopalan


title: Gene Expression Networks of Synchronized Cells Reveal Alzheimer's Disease in Autopsy-Validated Skin and Blood Samples

city: Morgantown

first: Florin

middle: V

last: Chirila

state: WV

address: 895 Vandalia Rd

department: Diagnostic

institute: Spot Dx

summary:
Late-onset Alzheimer’s disease (LOAD), which accounts for more than 95% of cases, lacks a well-defined gene expression signature, unlike early-onset forms caused by autosomal dominant mutations in PSEN1, PSEN2, and APP. Although early and late onset Alzheimer’s share core neuropathological features, their genetic convergence had not previously been demonstrated. In this study, synchronized skin fibroblasts from autopsy-confirmed LOAD patients revealed 20 significantly dysregulated genes (Adjusted P ≤ 0.05) that clearly distinguished LOAD from non-Alzheimer’s dementias. Among these, NHLH1, URB2, and WASF2 were also dysregulated in blood B lymphocytes, supporting a cross-tissue “modular resilience” framework. An additional 12 dysregulated gene families in skin were validated in blood, resulting in 15 LOAD-associated gene families shared across tissues.
Furthermore, five genes—CARNS1, NORAD, SCG2, SNHG14, and WASF2—were differentially expressed in skin fibroblasts and dysregulated in the prefrontal cortex, indicating a multi-layered resilience module connecting peripheral and central tissues. These genes participate in metabolic buffering, genomic stability, secretory organization, epigenetic regulation, and cytoskeletal remodeling. Their coordinated dysfunction suggests a systems-level impairment in stress adaptation relevant to AD biology.
Overall, the results reveal previously unrecognized gene-network convergence between familial early-onset and sporadic late-onset Alzheimer’s disease. The robust cross-tissue reproducibility of LOAD dysregulated gene networks highlights the potential of synchronized peripheral cells as accessible sources for disease-specific genomic profiling. This approach may enable the development of personalized biomarkers and targeted therapeutic strategies for Alzheimer’s disease.

overall_design: We aimed to uncover distinct networks of gene expression patterns using NGS RNA-Seq in synchronized skin fibroblasts and blood B-lymphocytes from autopsy-confirmed Alzheimer's disease (AD) patients, when compared to non-Alzheimer's disease dementia (non-ADD) patients.

first: William

last: MacTurk

first: Jack

last: Wallace

first: Guang

first: Daniel

last: Alkon


title: Exapted CRISPR-Cas12f homologs drive RNA-guided transcription

city: New York

first: Samuel

last: Sternberg

address: 701 W. 168th Street, HHSC 726

institute: Columbia University

summary: Bacterial transcription initiation is a tightly regulated process that canonically relies on sequence-specific promoter recognition by dedicated sigma (σ) factors, leading to functional DNA engagement by RNA polymerase (RNAP). Although the seven σ factors in E. coli have been extensively characterized, Bacteroidetes species encode dozens of specialized, extracytoplasmic function σ factors (σE) whose precise roles are unknown, pointing to additional layers of regulatory potential. Here we uncover an unprecedented mechanism of RNA-guided gene activation involving the coordinated action of σE factor in complex with nuclease-dead Cas12f (dCas12f). We screened a large set of genetically-linked dCas12f and σE homologs in E. coli using RIP-seq and ChIP-seq experiments, revealing systems that exhibited robust guide RNA enrichment and DNA target binding with a minimal 5ʹ-G target-adjacent motif (TAM). Recruitment of σE was dependent on dCas12f and guide RNA (gRNA), suggesting direct protein-protein interactions, and co-expression experiments demonstrated that the dCas12f-gRNA-σE ternary complex was competent for programmable recruitment of the RNAP holoenzyme. Remarkably, dCas12f-RNA-σE complexes drove potent gene expression in the absence of any requisite promoter motifs, with de novo transcription start sites defined exclusively by the relative distance from the dCas12f-mediated R-loop. Our findings highlight a new paradigm of RNA-guided transcription (RGT) that embodies natural features reminiscent of CRISPRa technology developed by humans.

sample_organism:
Escherichia coli
Flagellimonas taeanensis

overall_design:
E. coli ChIP-seq and RIP-seq profiling for 16 RNA-guided endonuclease-dead Cas12f proteins. ChIP-seq profiling for a subset of dCas12f-associated σE proteins. E. coli and F. taeanensis RNA-seq profiling.

UPDATE: [Mar-05-2026] The Fwd.bw and Rvs.bw files for Samples GSM8892747 to GSM8892789 were re-normalized.

first: Florian

last: Hoffmann

first: Tanner

last: Wiegand

first: Adriana

middle: I

last: Palmieri

first: Stephen

last: Tang

first: Juniper

last: Glass-Klaiber

first: Renjian

last: Xiao

first: George

middle: D

last: Lampe

first: Hoang

last: Le

first: Chance

last: Meers

first: Leifu

last: Chang

middle: H


title: Evolution of SARS-CoV-2 T cell responses as a function of multiple COVID-19 boosters

status: Public on Jul 29 2025

city: La Jolla

first: Alessandro

last: Sette

state: CA

address: 9420 Athena Cir

department: Center for Infectious Disease and Vaccine Research

institute: La Jolla Institute for Immunology

summary: We investigated the long-term impact of repeated COVID-19 vaccinations on adaptive immunity through a three-year study of 78 individuals without reported symptomatic infections. We observed distinct dynamics in Spike-specific responses across multiple vaccine doses. While antibody levels increased and stabilized with each booster, T cell responses quickly plateaued and remained stable. Notably, approximately 30% of participants showed evidence of asymptomatic infections. Single-cell RNA sequencing revealed a diverse landscape of Spike-specific T cell phenotypes, without signs of exhaustion or functional impairment. Individuals with evidence of asymptomatic infection displayed unique immunological features, including increased frequencies of Th17-like CD4+ T cells and GZMKhi/IFNR CD8+ T cell subsets. In this group, repeated vaccinations correlated with an increase in regulatory T cells, potentially indicating a balanced immune response that may mitigate immunopathology. By regularly stimulating T cell memory, boosters contribute to a stable and enhanced immune response, which may provide better protection against symptomatic infections.

overall_design: Single-cell RNA-seq profiling of CD4+ and CD8+ T cells reactive to SARS-CoV-2 Spike (S) as captured by applying the activation-induced marker (AIM) assay to PBMC samples from multiple visits (time-points) of 54 donors after receiving COVID-19 vaccine boosters and reporting no disease symptoms.

first: Ricardo

last: da Silva Antunes

first: Vicente

last: Fajardo-Rosas

first: Esther

last: Dawen Yu

first: Rosa Isela

last: Gálvez

first: Adam

last: Abawi

first: E. Alexander

last: Escarrega

first: Amparo

last: Martínez-Pérez

first: Emil

last: Johansson

first: Benjamin

last: Goodwin

first: April

last: Frazier

first: Jennifer

last: Dan

first: Shane

last: Crotty

first: Grégory

last: Seumois

first: Daniela

last: Weiskopf

first: Pandurangan

last: Vijayanand


title: scRNA sequencing analysis of neutrophils and sphingolipid pathway during virus persistence

city: Columbia

first: Bumsuk

last: Hahm

state: MO

address: NW301C Medical Sciences Building

department: Surgery-Research

institute: University of Missouri

summary: During lymphocytic choriomeningitis virus (LCMV) persistence, neutrophils were shown to be regulated, but the underlying mechanisms remain unclear. In this study, we have employed a scRNA analysis using bone marrow cells during LCMV infection. The experiment was conducted to define the possible role of sphingosine kinase 2 (SphK2) in neutrophil regulation upon LCMV infection. The findings may increase our understanding of viral mechanisms to regulate the host immunity and virus persistence.

overall_design: WT and Sphk2-/- knockout C57BL/6 mice (n=3 mice/group) were infected with LCMV Cl 13. Bone marrows cells were collected from uninfected WT and LCMV Cl 13-infected WT and Sphk2–/– mice at 3 dpi and analyzed using scRNA-seq.

first: Vijayamahantesh

last: Vijayamahantesh

first: Ying

last: He

first: Lei

last: Jiang

first: Hailey

last: Huerter

first: Kwang

last: Jung

first: Savannah

last: McKenna

first: Caleb

last: Studstill

first: Dong

last: Xu


title: DDX6 undergoes phase separation to modulate metabolic plasticity and drug resistance in AML

status: Public on Jul 27 2025

city: Duarte

first: Rui

last: Su

address: 1500 E Duarte Rd

institute: City of Hope

summary: DDX6 is a member of the DEAD-box helicase and it is highly expressed in acute myeloid leukemia (AML). The Knockout (KO) of DDX6 in AML cells significantly suppressed their growth, reduced their mitochondrial oxidative phosphorylation (OXPHOS) in vitro, and substantially delayed leukemogenesis in vivo. To delineate the molecular mechanism through which DDX6 exerts its biological functions in AML, we conducted transcriptome-wide RNA sequencing with Mono-mac-6 AML cells following DDX6 KO.

overall_design: We introduced the single-guide RNAs (sgRNAs) targeting DDX6 (sgDDX6-1 and sgDDX6-2) or the control sgRNA (sgNS) into Cas9 single-clone of Mono-mac-6 AML cells via lentivirus transduction. The transduction-positive AML cells were selected with blasticidin (10 μg/ml; Cat #: ant-bl-1, InvivoGen) and hygromycin B (200 μg/ml; Cat #: ant-hg-5, InvivoGen) for 1-2 weeks. DDX6 KO efficacy was confirmed by Western blot. Then, the total RNAs were extracted from each group with QIAzol and the poly(A)+ RNAs were enriched from total RNAs for library construction and sequencing. For each group, we included 2 replicates.

last: Dong

first: Hongjie

last: Bi


title: DEC1 Regulates Human β Cell Functional Maturation and Circadian Rhythm

status: Public on Jul 24 2025

city: Philadelphia

first: Mai

last: Liu

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: Stem cell-derived islet (SC-islet) organoids offer hope for cell replacement therapy in diabetes, but their immature function remains a challenge. Mature islet function requires the β-cell circadian clock, yet how the clock regulates maturation is unclear. Here, we show that a circadian transcription factor specific to maturing SC-β cells, DEC1, regulates insulin responsiveness to glucose. SC-islet organoids form normally from DEC1-ablated human pluripotent stem cells, but their insulin release capacity and glucose threshold fail to increase during in vitro culture and upon transplant. This deficit reflects downregulation of maturity-linked effectors of glucose utilization and insulin exocytosis, blunting glycolytic and oxidative metabolism, and is rescued by increasing metabolic flux. Moreover, DEC1 is needed to boost SC-islet maturity by synchronizing circadian glucose-responsive insulin secretion rhythms and clock machinery. Thus, DEC1 links circadian control to human β-cell maturation, highlighting its vitality to foster fully functional SC-islets.

overall_design: RNAseq of DEC1+/+ and DEC1-/- hPSC-islets at week 0, week 1, and week 2 of in vitro maturation by extended culture

first: Sam

last: Preza

first: Bliss

last: Zheng

first: Zihan

last: Gao

first: Akshaya

last: Biju

first: Juan

last: Alvarez-Dominguez


title: Single cell immunophenotyping of the Lyme erythema migrans lesion

city: New Haven

first: Hailong

last: Meng

state: CT

address: 300 George Str

institute: Yale University

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

overall_design: Refer to individual Series


title: Heterochronic transcription factor expression drives cone-dominant retina development in 13-lined ground squirrels.

status: Public on Jul 28 2025

first: Pin

last: Lyu

address: 400 N Broadway

institute: JHU

sample_organism:
Mus musculus
Ictidomys tridecemlineatus

platform_organism:
Mus musculus
Ictidomys tridecemlineatus


title: Sequential adaptive changes in a c-Myc-driven model of hepatocellular carcinoma

city: pittsburgh

first: Huabo

last: Wang

address: 4401 Penn Avenue

institute: Children hospital of pittsburgh

summary: Hepatocellular carcinoma (HCC) is a common cancer that frequently overexpresses the c-Myc (Myc) oncoprotein. Using a mouse model of Myc-induced HCC, we studied the metabolic, biochemical, and molecular changes accompanying HCC progression, regression, and recurrence. These involved altered rates of pyruvate and fatty acid β-oxidation and the likely re-directing of glutamine into biosynthetic rather than energy-generating pathways. Initial tumors also showed reduced mitochondrial mass and differential contributions of electron transport chain complexes I and II to respiration. The uncoupling of complex II's electron transport function from its succinate dehydrogenase activity also suggested a mechanism by which Myc generates reactive oxygen species. RNA sequence studies revealed an orderly progression of transcriptional changes involving pathways pertinent to DNA damage repair, cell cycle progression, insulin-like growth factor signaling, innate immunity, and further metabolic re-programming. Only a subset of functions deregulated in initial tumors was similarly deregulated in recurrent tumors thereby indicating that the latter can “normalize” some behaviors to suit their needs. An interactive and freely available software tool was developed to allow continued analyses of these and other transcriptional profiles. Collectively, these studies define the metabolic, biochemical, and molecular events accompanyingHCCevolution, regression, and recurrence in the absence of any potentially confounding therapies.

overall_design: Liver tissues were collected from a genetically engineered mouse model of hepatocellular carcinoma (FVB/N-Tg(tetO-MYC)36aBop/J × LAP-tTA) under seven experimental conditions. Mice were maintained on doxycycline (100 μg/ml) to suppress Myc expression. Tumor initiation was triggered by doxycycline withdrawal, and tissues were collected at day 3 (D3) and day 7 (D7) post-withdrawal, prior to visible tumor formation. Additional mice were maintained off doxycycline for 3–4 weeks until aggressive HCCs developed, after which tumors were sampled (Tumor group). Doxycycline was then reintroduced to induce regression, and tissues were collected after 3 days (R3) and 7 days (R7). A final group underwent long-term regression (2–3 months) followed by doxycycline withdrawal to induce tumor recurrence (Recurrence group). RNA-seq was performed on liver samples from each condition to profile gene expression during tumor progression, regression, and recurrence.

first: Edward

last: Prochownik


title: A cycling, progenitor-like cell population at the root of atypical teratoid rhabdoid tumor subtype differentiation trajectories [snATAC_data_tissue]

city: Bern

first: Irene

last: Paassen

address: Murtenstrasse 28

department: Biomedical Research

institute: Universität Bern

summary: Atypical teratoid rhabdoid tumors (ATRTs), characterized by the loss of SMARCB1, are among the most lethal pediatric brain tumors. Three molecular subtypes have been identified, each defined by distinct molecular and clinical features. Still, no subtype-specific treatments are available, highlighting the need to understand their inter and intra-subtype heterogeneity. Here, we generated a single-nucleus transcriptome atlas of ATRTs, validated with single-cell ATAC-seq and spatial transcriptomics, to study subtype-specific differentiation trajectories. We identified retained brain progenitor expression profiles within unique subtype-specific differentiation lineages. A shared cycling, progenitor-like cell population, interspersed throughout tumors, was observed across all ATRT patients. Finally, we demonstrate that subtype-specific differentiation trajectories can be induced pharmacologically in ATRT tumoroids directing tumor cells towards a non-proliferative, mature phenotype. Our study reveals that ATRT subtypes exhibit signaling trajectories mirroring normal fetal brain development, potentially enabling the development of maturation therapies tailored towards ATRTs.

overall_design:
Viably frozen samples were minced into small pieces and following 10X Genomics snMultiome pipeline after a nuclei were 7ADD+ sorted

***************************************************************
Raw files for human/patient samples are being made available in EGA (https://www.ebi.ac.uk/ega/) for controlled access to the personally identifiable sequence data.
***************************************************************

first: E

last: Blanco Carmona

first: I

first: Jiayou

last: He


title: A cycling, progenitor-like cell population at the root of atypical teratoid rhabdoid tumor subtype differentiation trajectories [snRNA_multiome_tissue]

first: Enrique


title: A cycling, progenitor-like cell population at the root of atypical teratoid rhabdoid tumor subtype differentiation trajectories [snMultiome_data_organoids]

overall_design:
ATRT tumoroid samples were made single cell and sorted for intact 7AAD+ nuclei. Following 10X Genomics snMultiome pipeline cells were processed for sequencing.

***************************************************************
Raw files for human/patient samples are being made available in EGA (https://www.ebi.ac.uk/ega/) for controlled access to the personally identifiable sequence data.
***************************************************************


title: A cycling, progenitor-like cell population at the root of atypical teratoid rhabdoid tumor subtype differentiation trajectories [Xenium Spatial_Transcriptomics]

overall_design: Formalin fixed paraffin embedded ATRT tissue sections were analyzed using the Xenium in situ Gene Expression platford for performing spatial transcriptomics (10X genomics)

first: J

last: DeMartino


title: Single-cell transcriptomic analysis reveals that inflammation drives the unfolded protein response during endocrine aging in mice

status: Public on Jul 25 2025

city: Beijing

first: Ran

last: Wei

address: Haidian District, Beijing Summer Palace Road No. 5

institute: Peking University

summary: The endocrine system severely impacts individual aging. However, its cellular signatures and underlying mechanisms have not been comprehensively elucidated. Here, we present a comprehensive single-cell transcriptomic atlas of six endocrine tissues from young and aged mice. Multiple aging-related pathways are disrupted in endocrine tissues, and the unfolded protein response (UPR) emerged as a key pathway related to endocrine aging. We found significant age-related expansion of exhausted GZMK+CD8+ T cells within endocrine tissues. Additionally, granzyme K (GZMK) signaling enhances the UPR and accelerates cellular senescence through the modulation of MHC-I expression in functional endocrine cells, revealing a novel regulatory axis of aging. Moreover, the inhibition of the GZMK receptor counteracts the UPR and endocrine aging. These findings establish an interplay between inflammation and the UPR in endocrine aging, offering profound insights into the underlying mechanisms of endocrine aging.

overall_design: We isolated the hypothalamus, pituitary glands, thyroid glands, adrenal glands, pancreas islets, and pineal glands from aged mice and young mice.

first: Zhehao

last: Du

first: Wei

last: Tao

first: Chen

last: Zhang


title: A cycling, progenitor-like cell population at the root of atypical teratoid rhabdoid tumor subtype differentiation trajectories [snRNA_10Xv3]

last: Blanco-Carmona


title: A cycling, progenitor-like cell population at the root of atypical teratoid rhabdoid tumor subtype differentiation trajectories [bulk RNA-Seq]

overall_design:
ATRT organoids were treated 48h with IC80 of drug compounds Entinostat, RO31-8220 mesylate, DMSO or thiostrepton and then harvested with trizol for RNA isolation

***************************************************************
Raw files for human/patient samples are being made available in EGA (https://www.ebi.ac.uk/ega/) for controlled access to the personally identifiable sequence data.
***************************************************************


title: Single-cell analysis defines heterogenous differentiation pathways of human innate T cells

status: Public on Jul 21 2025

city: Seoul

first: Suyeong

last: Park

address: 1, Gwanak-ro, Gwanak-gu, Seoul, Republic of Korea

department: College of Pharmacy

country: South Korea

institute: Seoul National University

summary: MAIT, NKT and γδ T cells are innnate-like T cells developed from thymic tissue. We used single cell RNA sequencing (scRNA-seq) to profile transcriptomic landscape of innate-like T cells in human thymus.

overall_design: Innate T cells from human thymic tissue were isolated by combination of Magentic-activated cell sorting (MACS) and Fluorescence-activated cell sorting (FACS) according to the presence or absence of tetramer binding affinity and analyzed using scRNAseq.


title: A cycling, progenitor-like cell population at the root of atypical teratoid rhabdoid tumor subtype differentiation trajectories


title: Single cell RNA sequencing of embryonic thymuses from 22q11.2 DS mouse models following in utero drug treatments.

city: Dallas

first: Nicolai

middle: S

last: van Oers

state: TX

address: NA2.200, 6000 Harry Hines Blvd

department: Immunology

institute: UT Southwestern Medical Center

summary: 22q11.2 DS causes the formation of a hypoplastic thymus. Mouse models of 22q11.2 were used to study the impact of different drugs, administered in pregnant mice,  on the growth of the thymus.  Thymuses from the different treatments were processed for single cell RNA sequencing. These were from control (Tbx1+/+;+/neo2) and 22q mouse models (Tbx1neo2/neo2 )

overall_design: Sc-RNA seq is performed on thymus cells isolated at E13.5 GA from a wild type embryo, Tbx1neo2/neo2 embryo, Tbx1neo2/neo2 embryo exposed in utero to Minoxidil drug and Tbx1neo2/neo2 embryo exposed in utero to PGE.2

first: Pratibha

last: Bhalla

first: Ashwani

last: Kumar

first: Chao

last: Xing


title: Transcriptional profiling of liver in cancer cachexia

status: Public on Jul 20 2025

city: Neuherberg

first: Peter

last: Weber

address: Ingolstädter Landstraße 1

country: Germany

institute: Helmholtz Zentrum München

summary: To study the response in the liver to cachectic and weight-stable cancer, we performed RNA-sequencing of whole liver nuclei and hepatocyte nuclei that were isolated using the INTACT methodology of weight stable NC26, pre-cachectic C26, cachectic C26, weight-stable MC38 and cachectic 8025 tumor bearing mice as well as their respective PBS controls.

overall_design: We implanted  cachexia-inducing tumor cells (C26, 8025) or tumor cells that give rise to weight-stable cancer (NC26, MC38) into syngenic Hep-INTACT mice. Livers were collected once a body weight loss of >10% was reached for C26 and 8025 tumor bearing animals at zeitgeber zeit (ZT) 9.

first: Mauricio

last: Berriel Diaz

first: Doris

last: Kaltenecker

first: Soren

last: Fisker Schmidt


title: ATAC-Seq of liver in cancer cachexia

summary: To study the response in the liver to cachectic and weight-stable cancer, we performed ATAC-sequencing of hepatocyte nuclei that were isolated using the INTACT methodology of weight stable NC26, pre-cachectic C26, cachectic C26, weight-stable MC38 and cachectic 8025 tumor bearing mice as well as their respective PBS controls.


title: Comparative Transcriptomic Analyses within FiveDevelopmental Stagesof the Mushroom Oudemansiella raphanipes

city: Lanzhou City

first: Lan

middle: Lan

last: Yu

state: Anning District

address: Northwest Normal University, Shi Street, Anning District, Lanzhou City, Gansu Province, China

department: College of Life Sciences

institute: Northwest Normal University

summary: In this paper, we have employed transcriptomic analysis as a pivotal tool to dissect the molecular landscape across the quintet of growth and developmental phases exhibited by Oudemansiella raphanipes. Our investigation has not only unveiled a suite of critical differentially expressed genes but also shed light on the nuanced nutritional attributes intrinsic to this fungal species. These findings promise to furnish fresh insights, serving as a beacon for the enhanced comprehension of O. raphanipes biology.

overall_design: Comparative gene expression profiling analysis using data obtained from RNA-seq of fifteen samples in the five growth stages

first: Yanjun

last: Ma

first: Lanlan

first: JingMing

first: YongXiang

last: Dang


title: Gene expression change after inactivation of ARHGAP45 by CRISPR-Cas9 and/or treatment of MBQ-167

city: PHILADELPHIA

first: Zhendong

last: Cao

address: BRB Rm620, 421 Curie Blvd

department: Cancer biology

institute: university of pennsylvania

summary: GTPase-activating proteins (GAPs) and guanine nucleotide exchange factors (GEFs) function as negative and positive regulators of small GTPases, orchestrating GDP/GTP-bound binary activity switches. Yet their functional significance in hematopoietic malignancies remains largely uncharted.  In our study, guided by single-cell transcriptomic analysis  and functional CRISPR screens in primary AML specimens and their derived models, we uncover an unexpected and selective oncogenic role for ARHGAP45 in AML. ARHGAP45 is upregulated in malignant cells while notably absent in healthy counterparts. Depletion of ARHGAP45 impedes AML growth and triggers myeloid differentiation but is dispensable for normal CD34+ hematopoietic stem/progenitor cells (HSPC) development. Using CRISPR-mediated epistasis screens, we further show that the ARHGEF1-RhoA-PKN1 axis is responsible for the ARHGAP45 phenotype. In addition, we further found that ARHGAP45 prevents RhoA overactivation, loss of cell polarity, and lineage commitment. On the other hand, our screens also unveil the synergistic effect of combinatorial ARHGAP45 and CDC42 inhibition, which we further validate in vitro and in vivo. Collectively, our studies reveal that ARHGAP45 is indispensable for leukemia stemness and aggressiveness and rationalize therapeutic strategies for modulating GAP and GTPase activity in AML.

overall_design: mRNA profiles of Cas9 sgRNA-expressing human cell lines and PDX cells

first: Pu


title: RNA Seq of hearts upon hepatocyte-specific overexpression of REV-ERBα in cancer cachexia

summary: We evaluated the transcriptional response in the heart upon hepatocyte-specific overexpression of REV-ERBα in the C26 cancer cachexia model.

overall_design: We injected AAV intravenously that express either GFP or REV-ERBα  under the control of the hepatocyte specific promoter Tbg, followed by a subcutaneous transplantation of C26 tumor cells 10 days later. Non-tumor bearing mice received a PBS injection


title: Heterochronic transcription factor expression drives cone-dominant retina development in 13-lined ground squirrels. [scRNA-Seq]

first: Pin

last: Lyu

summary: Evolutionary adaptation to diurnal vision in ground squirrels has led to the development of a cone-dominant retina, in stark contrast to the rod-dominant retinas of most mammals. The molecular mechanisms driving this shift remain largely unexplored. Here, we perform single-cell RNA sequencing (scRNA-Seq) and chromatin accessibility profiling (scATAC-Seq) across developmental retinal neurogenesis in the 13-lined ground squirrel (13LGS) to uncover the regulatory basis of this adaptation. We find that 13LGS cone photoreceptors arise not only from early-stage neurogenic progenitors, as seen in rod-dominant species like mice, but also from late-stage neurogenic progenitors. This extended period of cone generation is driven by a heterochronic shift in transcription factor expression, with cone-promoting factors such as Onecut2, Pou2f1, and Zic3 remaining active in late-stage progenitors, while cone-differentiation factors Thrb, Rxrg, and Mef2c are expressed precociously in cone specification. Functional analyses reveal that Zic3 and Mef2c promote cone specification, acting through species-specific regulatory elements that drive their expression in late-stage progenitors. These results demonstrate that evolutionary modifications to gene regulatory networks underlie the development of cone-dominant retinas, providing insight into mechanisms of sensory adaptation and potential strategies for cone photoreceptor regeneration in vision disorders.

overall_design: In 13LGS, retinal neurogenesis begins around embryonic day 18 (E18), with birth occurring at E27 (blue-dotted line in Fig. 1A), and concludes by postnatal day 17 (P17)27. To comprehensively profile cellular-level changes in gene expression and chromatin accessibility, we conducted scRNA-Seq and scATAC-Seq analyses across ten developmental time points, spanning the full course of neurogenesis and the immediate post-neurogenesis period (E18–P21).

first: Kurt

last: Weir

first: Sangeetha

last: Kandoi

first: Roujin

last: An

first: Nicole

last: Pannullo

first: Isabella

last: Palazzo

first: Jared A.

last: Tangeman

first: Jun

last: Shi

first: Steven H.

last: DeVries

first: Dana K.

last: Merriman

first: Jiang

last: Qian

first: Seth

last: Blackshaw


title: Cholinergic Signaling Modulates Intestinal Pathophysiology in a Drosophila Model of Cystic Fibrosis

status: Public on Jul 16 2025

city: Boston

first: Yanhui

last: Hu

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

summary: Cystic Fibrosis (CF) is a genetic disease caused by mutations in the CFTR gene, which affects cells in organs like the lungs, pancreas, and gut. Treatments aim to fix the CFTR protein, but many gut issues remain untreated. In this study, we use fruit flies (Drosophila) as a model to study the effects of losing CFTR specifically in the gut. We show that knocking down CFTR in gut cells leads to problems seen in CF, such as poor gut movement, trouble absorbing nutrients, and low energy levels. Using RNA sequencing, we find that CF guts have higher levels of the gene acetylcholine esterase (Ace), which lowers cholinergic (nerve signal) activity. Experiments confirm that CF guts are less sensitive to cholinergic signals, but reducing Ace brings back normal gut function. We also find a transcription factor called Forkhead (Fkh), similar to human FOXA1/2, that increases Ace in CF. Our study shows that the fruit fly gut is a useful model for studying CF in the gut, and suggests that boosting cholinergic signaling could help treat gut problems in CF.

overall_design: Fruit flies (Drosophila) was used to perform enterocyte-specific knockdown of CFTR gene to model CF gut pathology. Gut movement, nutrient absorption, and energy levels were assessed. Single-nuclei RNA sequencing (snRNA-seq) was performed to identify gene expression changes, revealing increased expression of acetylcholine esterase (Ace). Functional assays tested cholinergic signaling and showed that Ace knockdown could restore gut function. Finally, the role of the transcription factor Forkhead (Fkh) in regulating Ace was investigated.

first: Liz

last: Lane

first: Mujeeb

last: Qadiri

first: Norbert

last: Perrimon


title: PELO-1/Pelota-mediated ribosome-associated quality control counteracts aging and age-associated pathologies across species.

status: Public on Jul 22 2025

city: Daejeon

first: Seung-Jae

last: Lee

address: 291, Daehak-ro, Yuseong-gu, Daejeon, Republic of Korea

institute: Korea Advanced Institute of Science and Technology

summary: Ribosome-associated quality control (RQC) is a pivotal biological process that governs the fidelity of mRNA homeostasis and protein synthesis. Here, by focusing on PELO-1/Pelota, the ribosome rescue factor crucial for RQC and mRNA surveillance, we sought to determine how RQC and the mRNA surveillance contributed to longevity and the prevention of premature aging and age-associated diseases. We performed RNA sequencing (RNA seq) analysis that compared the transcriptome of long-lived daf-2(-) with that of short-lived daf-2(-) pelo-1(-); skih-2(-) mutant C. elegans.

overall_design: The investigation of the changes of gene expression in long-lived daf-2(-) with that of short-lived daf-2(-) pelo-1(-); skih-2(-) mutant C. elegans.

first: Jongsun

first: Eun Ji

last: Kim

first: Seokjin

last: Ham


title: Classically activated macrophages undergo functionally significant nucleotide metabolism remodelling driven by nitric oxide

city: Madison

first: Jing

last: Fan

state: WI

address: 330 N Orchard St., Fan Lab

department: Metabolism

institute: Morgridge Institute for Research

summary: During an immune response, macrophages specifically reprogramme their metabolism to support functional changes. Here, we revealed that nucleotide metabolism is one of the most significantly reprogrammed pathways upon classical activation. Specifically, de novo synthesis of pyrimidines is maintained up to uridine monophosphate, but blocked at cytidine triphosphate and deoxythymidine monophosphate synthesis; de novo synthesis of purines is shut off at the last step (catalysed by AICAR transformylase/IMP cyclohydrolase), and cells switch to increased purine salvage. Nucleotide degradation to nitrogenous bases is upregulated but complete oxidation of purine bases (catalysed by xanthine oxidoreductase) is inhibited, diverting flux into salvage. Mechanistically, nitric oxide was identified as a major regulator of nucleotide metabolism, simultaneously driving multiple key changes, including the transcriptional downregulation of Tyms and profound inhibition of AICAR transformylase/IMP cyclohydrolase and XOR. Inhibiting purine salvage using HGPRT knockout or inhibition alters the expression of many stimulation-induced genes, suppresses macrophage migration and phagocytosis, and increases the proliferation of the intracellular parasite Toxoplasma gondii. Together, these results thoroughly uncover the dynamic reprogramming of macrophage nucleotide metabolism upon classical activation and elucidate the regulatory mechanisms and functional significance of such reprogramming.

overall_design: To investigate how gene expression changes in Hprt Knockout macrophages, RNA was collected from both wild-type and Hprt Knockout macrophages that were either unstimulated or stimulated with LPS+IFNy for 48h.

first: Steven

last: John

first: Gretchen

last: Seim

first: Billy

last: Erazo-Flores

first: James

middle: A

last: Votava

first: Uzziah

last: Urquiza

first: Nicholas

last: Arp

first: John

last: Steill

first: Jack

last: Freeman

first: Lauren

middle: N

last: Carnevale

first: Isaiah

last: Roberts

first: Xin

last: Qing

first: Stuart

last: Lipton

first: Ron

last: Stewart

first: Laura

last: Knoll


title: Revisiting oxygen toxicity: evolution and adaptation to superoxide in a SOD-deficient bacterial pathogen [paraquat]

status: Public on Jul 15 2025

city: Paris

first: Marc

last: Monot

address: 28 rue du docteur roux

institute: Institut Pasteur

summary: Defenses against oxidants are crucial for the virulence of pathogens, with superoxide scavenging enzymes (SOSEs) playing a vital role for most aerobes. However, our knowledge of superoxide adaptation primarily stems from the study of SOSE-encoding bacteria. Here, we investigated the evolution of a naturally SOSE-deficient pathogen (Leptospira spp.), along with the alternative mechanisms it recruits to combat superoxide stress. We demonstrate that emergence of pathogenic Leptospira correlated with SOD loss, but that a long-lasting adaptation to superoxide remains possible. We reveal that cysteine and leucine biosynthesis are the most induced pathways in response to superoxide and demonstrate the importance of sulfur metabolism in superoxide adaptation  in this SOSE-deficient model. We also propose cysteine oxidation as a key mediator of superoxide toxicity in the absence of SOSEs. This study challenges our conventional understanding of the oxygen toxicity theory and proposes a new model of superoxide adaptation through metabolic rewiring in bacteria.

overall_design: To identify superoxide-induced mechanisms in pathogenic Leptospira, RNA-seq analyses were performed on L. interrogans exposed to 10 and 50 M of paraquat.

first: Samuel

middle: G

last: Huete

first: Nadia

last: Benaroudj


first: Jing

last: Fan

overall_design: To investigate how gene expression changes in macrophages over a timecourse of stimulation, wild-type bone-marrow derived macrophages were treated with an acute (2h) LPS+IFNy stimulation. Then the stimulants were washed off and RNA was collected from macrophages at various time points after initial stimulation.

first: Steven

last: John

middle: J


title: Translational activators align mitochondrial mRNAs at the small ribosomal subunit for translation initiation

first: Mary

middle: T

last: Couvillion

summary: Mitochondrial gene expression is essential for oxidative phosphorylation. Mitochondrial-encoded mRNAs are translated by dedicated mitochondrial ribosomes (mitoribosomes), whose regulation remains elusive. In the baker´s yeast Saccharomyces cerevisiae, nuclear-encoded mitochondrial translational activators (TAs) facilitate transcript-specific translation by a yet unknown mechanism. Here, we investigated the function of TAs containing RNA-binding pentatricopeptide repeats (PPRs) using selective mitoribosome profiling and cryo-EM structural analysis. These analyses revealed that TAs exhibit strong selectivity for mitoribosomes initiating on their target transcripts. Moreover, TA-mitoribosome footprints indicated that TAs recruit mitoribosomes proximal to the start codon. Two cryo-EM structures of mRNA-TA complexes bound to post-initiation/pre-elongation-stalled mitoribosomes revealed the general mechanism of TA action. Specifically, the TAs bind to structural elements in the 5' UTR of the client mRNA as well as to the mRNA exit channel to align the mRNA in the small subunit during initiation. Our findings provide a structural basis for understanding how mitochondria achieve transcript-specific translation initiation without relying on general sequence elements to position ribosomes at start codons.

overall_design: Mitochondrial selective ribosome profiling of translational activators and related factors in S. cerevisiae cells

first: Joseph

last: Bridgers

first: Andreas

last: Carlstrom

first: Dawafuti

last: Sherpa

first: Jingjing

last: Gao

first: Bowen

last: Wan

first: Sichen

last: Shao

first: Martin

last: Ott

first: Stirling

last: Churchman


title: Adverse proinflammatory responses in the kidney after FGF23 administration in murine kidney disease models

first: Matthias

middle: B.

last: Moor

address: Freiburgstrasse

institute: University Hospital Bern

summary: FGF23 is a biomarker associated with morbidity and mortality, but controversies remain if a causative link exists between FGF23 excess and adverse renal consequences in chronic kidney disease (CKD).  Here, we investigated renal FGF23 signaling in kidney disease models in mice, with a focus on adverse pro-inflammatory effects assessed in bulk transcriptomes.

overall_design: To investigate renal effects of FGF23 hormone in kidney disease, we assessed bulk transcriptomes in kidney of FGF23 or vehicle treated mice that were i) healthy males or males with anti-glomerular basement membrane disease receiving 6 days of treatments, ii) healthy females or females with adriamycin nephroathy receiving 24h of treatment, and iii) adenine nephropathy mouse kidney tissue receiving ex vivo treatment for 1h in precision-cut kidney slices (PCKS).

middle: B

first: Mikhail

last: Burmakin

first: Jaakko

last: Patrakka

first: Hannes

last: Olauson


title: Comparative Evaluation of miRNA Detection in Plasma, Urine, and Liquid-Based Cytology (LBC) for High-Grade Cervical Intraepithelial Neoplasia

status: Public on Jul 08 2025

city: Barretos

first: Stéphanie

last: Calfa

state: São Paulo

address: Antenor Duarte Viléla, 1331 - Dr. Paulo Prata

country: Brazil

institute: Barretos Cancer Hospital

summary: We profiled 798 miRNAs using NanoString technology in plasma, urine, and liquid-based cytology (LBC) from 24 women with and without high-grade cervical lesions (CIN2/3). LBC showed the highest detection efficiency and consistency, with the lowest proportion of low-count miRNAs and the highest expression levels, supporting its utility as the most effective specimen type for miRNA-based screening.

overall_design: In the study presented here, matched plasma, urine, and liquid-based cytology (LBC) samples were collected from 24 women—12 with high-grade cervical intraepithelial neoplasia (CIN2/3) and 12 controls. Expression profiling of 798 miRNAs was performed using the NanoString nCounter Human v3 miRNA panel to compare detection performance across specimen types.

first: Ana Julia

last: Freitas

first: Welinton

last: Hirai

first: Rhafaela

middle: L

last: Causin

first: Júlio César

last: Possati-Resende

first: Ricardo

last: Reis

first: Rui

middle: M

first: Márcia Maria

middle: C

last: Marques


title: PbAP2-TR plays a role in regulating major transcriptomic changes from early to late trophozoite [PbAP2-TR_DIP-seq]

status: Public on Jul 01 2025

city: tsu

first: masao

last: yuda

state: mie

address: edobashi 2-174

institute: mie university

summary: To investigate the DNA-binding property of AP2 domains of PbAP2-TR, DNA immunoprecipitation followed by high-throughput sequencing (DIP-seq) analysis was performed. Recombinant AP2 domains 1–2 or AP2 domain 3 fused with maltose-binding protein (MBP) were mixed with the P. berghei genomic DNA fragmented via sonication, and protein-DNA complex was harvested using amylose resin. The obtained DNA fragments were sequenced via the next generation sequencing.

overall_design: DNA fragments encoding the AP2 domains 1–2 or AP2 domain 3 of PbAP2-TR were each cloned into the expression vector pMal-c5X (NEB). Escherichia coli strain DH5α transformed with these plasmids was cultured for 12 h at 37 °C. Next, expression of the MBP-fused protein was induced by adding isopropyl β-D-thiogalactopyranoside (final concentration of 200 nM) in the culture and incubating for 9 h at 25 °C. Recombinant AP2 domains fused with MBP was purified using amylose resin, and eluted with 10 mM maltose solution. Subsequently, the MBP-fused homeodomain was incubated with P. berghei ANKA genomic DNA fragments in binding/washing buffer (10 μM ZnSO4, 2 mM MgCl2, 2 mM Tris-HCl at pH 7.4, 100 mM KCl, and 10% glycerol) for 30 min. The protein/DNA solution was further mixed with amylose resin and incubated for 30 min. After incubation, the resin was washed three times with binding/washing buffer, and bound protein-DNA complexes were eluted with 10 mM maltose solution. A sequencing library was prepared from the DNA fragments and sequenced using Illumina NextSeq. Before their use for DIP, genomic DNA fragments were also sequenced as an input, the raw data of which have been already deposited on Gene Expression Omnibus under the accession number GSE159045.

first: Tsubasa

last: Nishi

first: Izumi

last: Kaneko

first: Shiroh

last: Iwanaga

first: Masao

last: Yuda


title: PbAP2-TR plays a role in regulating major transcriptomic changes from early to late trophozoite [PbAP2-TR_RNA-seq]

summary: Plasmodium berghei transcriptomes of pbap2-tr-DiCre, a parasite line in which pbap2-tr is disrupted by DiCre-mediated recombination in the presence of rapamycin, were analyzed at the trophozoite stage.

overall_design: pbap2-tr-DiCre parasites treated with 30 nM rapamycin or DMSO were harvested at 12 h post-injection (hpi), and total RNA was extracted from the parasites. Libraries were constructed from the total RNA and then sequenced by the next generation sequencing.


title: An image-based transcriptomic atlas of the mouse gut reveals spatial, regional, and microbiota-dependent fine-tuning

status: Public on Jul 18 2025

first: Jeffrey

last: Moffitt

address: 200 Longwood Ave

department: Program in Cellular and Molecular Medicine

institute: Boston Children's Hospital

summary: The gastrointestinal tract (GI) is a remarkably complex environment comprising a diverse array of cell types, microbes, and bioactive small molecules. To shed new light on how the gut is organized and senses its environment, we constructed a spatially resolved single-cell atlas of the mouse lower digestive tract using MERFISH with a specific focus on the thousands of receptors involved in small molecule sensation and microbial pattern recognition. We identified expected and novel cell types and charted their spatial organization across four GI regions. In addition, we discovered receptor expression gradients and heterogeneity cued by spatial location, and overall revealed divergent sensing capabilities across gut cell types, regions, and spatial contexts. In addition, we charted the remodeling of these features that occurs in the absence of the microbiome. Our atlas opens a new window into the molecular and cellular organization of gut sensation, which, given the pharmacological relevance of many receptors, may provide a clinically relevant resource.

overall_design: To provide an in-house measurement of gene expression in the SPF intestine as a validation for MERFISH results, distal colon tissue was harvested from C57BL/6NTac mice, flushed and rinsed with 4 mM ribonucleoside vanadyl complex (RVC; New England Biolabs [NEB] S1402S) in 1 x phosphate-buffered saline (PBS; ThermoFisher Scientific[Thermo] AM9625) at 4 oC. The tissue was then dissolved in TRIzol™ (Thermo 15596026) and RNA extraction was performed by the Direct-zol RNA Miniprep Plus kit (Zymo R2071), followed by low input library preparation and paired-end sequencing by Illumina NextSeq 500. To analyze these data, we used tophat (v2.1.1) and cufflinks (v2.2.1) with default parameters, aligning to the mouse genome (GRCm39).

first: Rosalind

last: Xu

middle: R


title: Revisiting oxygen toxicity: evolution and adaptation to superoxide in a SOD-deficient bacterial pathogen

first: Marc

last: Monot

overall_design: RNAs will be prepared from 3 replicates of the resistant L. interrogans strain and 3 replicates of the original clone before adaptation and RNAseq will be performed.

first: Samuel

last: Huete

first: Rania

last: Ouazahrou

first: Nadia

last: Benaroudj


title: Dasatinib Overcomes Acquired Resistance to BRAF/MEK Inhibitor Therapy

first: Priyankara

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Despite high initial activity, resistance to combination BRAF/MEK inhibitor (BRAFi/MEKi) therapy arises in virtually all patients with BRAFV600E/K melanoma. There remains a critical unmet need to identify strategies to overcome acquired BRAFi/MEKi resistance. To better personalize therapy in cancer patients and address therapy relapse, umbrella trials have commenced whereby genomic sequencing of a panel of potentially actionable targets guide therapy selection for patients. However, the superior efficacy of such approaches remains to be seen. We here test the robustness of the umbrella trial rationale by analyzing relationships between genomic status of a gene and the downstream consequences at the protein level of related pathways, and find poor relationships between mutations, copy number amplification, and protein expression and activation.  To profile candidate therapeutic strategies that may offer clinical benefit in the context of acquired BRAFi/MEKi resistance, we utilized a repository of patient-derived xenograft models from heavily pretreated patients with resistance to BRAFi/MEKi and/or immunotherapy (R-PDX). With these R-PDXs, we executed in vivo compound repurposing screens using 11 FDA-approved agents from an NCI-portfolio with pan-RTK, non-RTK and/or PI3K-mTOR specificity. We identify dasatinib as capable of restoring sensitivity to BRAFi/MEKi in ~70% of R-PDX models tested. Elevated baseline protein expression of canonical drivers of therapy resistance (e.g., AXL, YAP, HSP70, phospho-AKT) predicts BRAFi/MEKi plus dasatinib treatment sensitivity. We therefore propose that dasatinib plus BRAFi/MEKi combination therapy may restore antitumor efficacy in patients that have relapsed to standard-of-care therapy by broadly targeting proteins critical in melanoma therapy escape. Further, we submit that this experimental PDX paradigm could potentially improve preclinical evaluation of therapeutic modalities and augment our ability to identify biomarker-defined patient subsets that may respond to a given clinical trial. Furthermore, the aged patient population has suboptimal responses to SARS-CoV-2 vaccine antigens. Here, we characterize vaccine-induced responses to SARS-CoV-2 synthetic DNA vaccine antigens in 18-month-old mice and interrogate protection. Aged mice have altered cellular responses, including decreased IFNγ secretion and increased TNFα secretion as compared to young mice. Aged mice had significantly decreased binding and neutralizing antibodies in their serum compared to their young counterparts. Co-immunization with the plasmid-encoded molecular adjuvant adenosine deaminase-1 (pADA) enhanced cellular responses and expanded the breadth of humoral responses in aged mice. pADA co-delivery also altered the gene expression profiles of lymph node lymphocytes in aged animals. Upon challenge pADA co-immunization modestly decreased age-associated morbidity and mortality in ACE2 transgenic and mouse-adapted SARS-CoV-2 challenge models. These data support the use of aged mice as a model for age-associated decreased vaccine immunogenicity and infection-mediated morbidity and mortality in the context of SARS-CoV-2 and provide further support of the use of adenosine deaminase as a molecular adjuvant.

first: Rebecca

middle: W

last: Vito

first: Herlyn

last: Mennhard


title: Evalation of Vitamin D and Doxercalciferol Effect on Uterine Fibroid Growth

status: Public on Jul 02 2025

city: Valencia

first: Ana

last: Corachán

state: València

address: Avenida Fernando Abril Martorell, 106, torreA, Planta 7

country: Spain

institute: IVIRMA Global Research Alliance, IVI Foundation, IIS La Fe

summary: Uterine fibroids (UF) are the most common pelvic tumor in women of reproductive age. Despite its high prevalence, there is an unmet need in the field for a non-hormonal fertility-friendly anti-fibroid treatment. Vitamin D deficiency has been linked to a higher risk of UF, and its efficiency as a treatment to reduce UF size has been demonstrated in vitro and in vivo. However, long-term vitamin d treatments could induce hypercalcemia, and vitamin D analogs have been proposed as an alternative since they show less calcemic activity. Our study aims to describe the signaling pathways and molecular mechanisms by which Vitamin D (VD3) and Doxercalciferol (a Vitamin D analog) (DCL) reduces UF size in a UF patient-derived xenograft (PDX).

overall_design: MED12-mutant human uterine fibroids (UF) were collected from African American women undergoing hysterectomy or myomectomy for symptomatic UF (n=10). Female NOD-SCID mice (n=14) were used to generate the PDX mouse model. Mice were hormonally supplemented with 60-day release pellets with 17ß-estradiol (0.2 mg) and progesterone (50 mg). One week after the xenograft surgery, animals were treated for 6 weeks with the bioactive form of Vitamin D3 (VD3), 1α,25(OH)2D3 and the synthetic Vitamin D2 analog Doxercalciferol (DCL). According to the treatment two different studies were conducted: 1) VD3 0.5 µg/kg/day (n=3) and 2) DCL 0.3 µg/kg/day (n=4). Each study had her own control group, in which animals were treated with the corresponding drug vehicle. At the end of the treatment, animals were euthanized and UF xenografts were collected. Each study had her own control group, in which animals were treated with the corresponding drug vehicle.

first: Maria

middle: V

last: Bariani

first: Mohamed

last: Ali

first: Qiwei

last: Yang

first: Hortensia

last: Ferrero

first: Ayman

last: Al-Hendy


title: PbAP2-TR plays a role in regulating major transcriptomic changes from early to late trophozoite [pbap2-g_KO_RNA-seq]

first: masao

last: yuda

summary: Plasmodium berghei transcriptomes of gametocyte-absent mutant parasites, the pbap2-g-knockout line (pbap2-g(-)), were analyzed from ring to trophozoite stages by high-throughput RNA sequencing (RNA-seq) analysis.

overall_design: Cell cycle of pbap2-g(-) parasites was synchronized, and the parasites were harvested for total RNA extraction at 4, 8, 16 h post-injection. Libraries were constructed from the total RNA and then sequenced by the next generation sequencing.

first: Tsubasa

last: Nishi

first: Izumi

last: Kaneko

first: Shiroh

last: Iwanaga


title: The c-MYC-WDR43 signalling axis promotes chemoresistance and growth in colorectal cancer by inhibiting p53 activity

city: Guangzhou

first: Ziyang

last: Wang

state: --- Select One ---

address: 58 Zhongshan 2nd Road

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

summary: Colorectal cancer (CRC) is one of the most common malignancies worldwide. Oxaliplatin chemoresistance is a major challenge in the clinical treatment of CRC. Through bioinformatics analysis, we identified WDR43 as a critical potential oncogenic factor in CRC pathogenesis. Clinically, WDR43 is highly expressed in CRC, and WDR43 overexpression is associated with poor prognosis in CRC patients. WDR43 knockdown significantly inhibits cell growth by arresting the cell cycle and enhances the effect of oxaliplatin chemotherapy capacities in vitro and in vivo. Mechanistically, upon oxaliplatin stimulation, c-MYC promotes the transcriptional regulation and expression of WDR43. WDR43 enhances the ubiquitination of p53 by MDM2 by binding RPL11, thereby reducing the stability of the p53 protein, which further induces the proliferation and chemoresistance of CRC cells. Thus, WDR43 may not only mark CRC progression but also be a potential therapeutic target of chemoresistance in CRC.

overall_design: WDR43 were knocked down in HCT116 cells, and the differences in gene expression were compared with shNC, respectively, using RNAseq.

first: Yuqin

last: Di

first: Weiling

last: He


title: PbAP2-TR plays a role in regulating major transcriptomic changes from early to late trophozoite [PbAP2-TR_ChIP-seq]

summary: To investigate the genome-wide binding sites of PbAP2-TR and PbMORC in the asexual blood stage of Plasmodium berghei, the chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) analyses were performed. Parasites expressing GFP-fused PbAP2-TR or GFP-fused PbMORC were generated from the Cas9-expressing parasite (PbCas9), and pbap2-g was disrupted in these parasites (PbAP2-TR::GFPpbap2-g(-) and PbMORC::GFPpbap2-g(-)). Whole blood was harvested from mice infected with these transgenic parasites at 12 h post infection,and the parasites were then subjected to ChIP-seq experiments using anti-GFP antibody. Genome-wide binding sites of PbAP2-TR were determined from the sequence data.

overall_design: PbAP2-TR::GFPpbap2-g(-) and PbMORC::GFPpbap2-g(-) parasites were each cultured for 16 h, and schizonts formed in the cultures were injected into mice. Chromatins associated with GFP-fused PbAP2-TR or PbMORC were IPed with anti-GFP antibody, and DNA fragments purified from the IPed chromoatins were sequenced by the Next Generation Sequencing. Using non-IPed samples as a control (INPUT), binding sites of PbAP2-TR were determined from the sequence data.

first: Masao

last: Yuda


title: Opposing role of phagocytic receptors MERTK and AXL in Progranulin deficient FTD

status: Public on Jun 30 2025

city: New York

first: Li

last: Gan

state: NY

address: 413 East 69th Street, 9th Floor BB904

department: Helen and Robert Appel Alzheimer’s Disease Research Institute

institute: Weill Cornell Medicine

summary: Genetic mutations in the progranulin gene, GRN, cause frontotemporal dementia and a lysosomal storage disorder. Using single-nuclei RNA sequencing of the post-mortem brain tissue from heterozygous pathogenic granulin variant (GRN+/-) carriers we found dysregulation of microglia, phagocytosis and the phagocytic receptors MERTK and AXL. Exogenous progranulin regulated MERTK and AXL RNA expression in human microglia induced from iPSCs irrespective of GRN mutation status, without directly binding to MERTK or AXL proteins. We generated double knock-out mice and found that constitutive homozygous loss of Grn and Mertk (Grn-/-;Mertk-/-) rescued microglial disease signature while constitutive homozygous loss of Grn and Axl (Grn-/-;Axl-/-) worsened the microglial disease signature. Higher levels of AXL protein, but not MERTK protein, in the post-mortem superior temporal gyrus correlated with worse cross-sectional functional impairment (CDR sum of boxes) by both GRN+/- mutation carriers and non-carrier controls. These data explain in part the inflammation seen in GRN-FTD and are applicable to other inflammatory states in which PGRN, MERTK and AXL play regulatory roles, including cancer, sepsis, stroke, diabetes and obesity. The interaction between GRN, MERTK and AXL opens potential new therapeutic avenues to intervene on this inflammatory axis.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Droplet-based single nuclear RNA sequencing from superior frontal gyrus from 7 patients with GRN+/- loss of function mutations and 8 GRN+/+ aged controls without neurological disease; thalamic cells from WT control, single KO mice (Grn-/-, Mertk-/- and Axl-/- mice) and double KO mice (Grn-/-;Mertk-/- and Grn-/-;Axl-/-).

first: Claire

last: Clelland

last: Fan

first: Jon

middle: I

last: Etchegaray

first: Chad

last: Altobelli

first: Sally

middle: E

last: Salomonsson

first: Alisha

last: Maltos

first: Aradhana

last: Sachdev

first: Yaqiao

last: Li

first: Yungui

last: Zhou

first: David

last: Le

first: Chao

first: Gillian

last: Carling

first: Lay

last: Kodama

first: Faten

last: Sayed

first: Juan

last: Perez-Bermejo

first: Ethan

last: Geier

first: Jennifer

last: Yokoyama

first: Howie

last: Rosen

first: Alissa

last: Nana

first: Salvatore

last: Spina

first: Lea

last: Grinberg

first: William

last: Seeley

first: Fanny

last: Elahi

first: Michelle

last: Arkin


title: Loss of Snhg5 disrupts cell-cycle regulation without altering cystogenesis in a mouse model of polycystic kidney disease.

city: Stony Brook

first: Karam

last: Aboudehen

address: 101 Nicolls Rd, HSC T 15-112

department: Division of Nephrology & Hypertension

institute: Stony Brook University

summary: Long non-coding RNAs (lncRNAs) regulate diverse cellular pathways and are increasingly linked to human disease. Snhg5 is frequently described as a pathogenic lncRNA in many human diseases, including cancer. Our previous studies revealed that Snhg5 is one of the most upregulated lncRNAs in multiple mouse models of polycystic kidney disease (PKD). Yet its role in renal biology and in autosomal dominant PKD (ADPKD) is not known. To elucidate the role of Snhg5, we generated a global Snhg5-null mouse. Homozygous animals were viable and displayed normal kidney morphology and function. RNA-sequencing of Snhg5-null kidneys and renal epithelial cells revealed common alterations in gene expression linked to cell cycle progression and DNA replication. At the molecular level, Snhg5-null cells showed an increased mitotic fraction, coinciding with depletion of ARPC5—a core ARP2/3 subunit— suggesting that reduced ARPC5 may contribute to this phenotype. To determine whether Snhg5 upregulation is pathogenic in mouse PKD, we crossed Snhg5-null mice with a collecting duct-specific Pkd1-mutant mouse model. Loss of Snhg5 did not attenuate cyst formation; if anything, disease severity was mildly but not significantly exacerbated. These findings indicate that Snhg5 modulates mitotic control and is dispensable for kidney development and cystogenesis in collecting duct-derived cysts.

overall_design: RNA-sequencing profiling of in vitro wild-type and Snhg5 knockout mIMCD3 cells, and in vivo wild-type and Shng5 knockout mouse kidneys.

first: Stephen

last: D'Amico


title: Lung tissue-resident memory T cells optimize protection by IL-10 regulation of innate immunity

first: Donna

last: Farber

address: 701 W168th street

institute: Columbia University

summary: Respiratory viral infections establish tissue resident memory T (TRM) cells in the lung, which provide optimal protection against infectious challenge, though the underlying mechanisms remain incompletely understood. Here, using a mouse model of heterosubtypic influenza infection, we demonstrate that the lung-localized secondary immune response exhibits an attenuated innate immune response compared to the primary response due to TRM-mediated production of the immunoregulatory cytokine IL-10. Using reporter mice, we identify that lung TRM are the predominant producers of early IL-10 in response to viral challenge. Inhibition of early IL-10 signaling in secondary infections results in increased morbidity and lung pathology, and reveals pleiotropic effects of IL-10 in regulating macrophage inflammation and enhancing IFN-g production by memory CD8+T cells. Human influenza-specific TRM isolated from lungs recapitulate robust IL-10 expression associated with augmented effector responses of murine TRM. These data support a dual role for TRM in coordinating in situ secondary responses - augmenting effector responses for robust viral clearance while dampening inflammation to limit tissue damage.

overall_design: There are two experiments of data submitted here. The goals of these experiments were to determine the effect of either (1) previous infection or (2) IL-10 signaling blockade on the lung-localized immune response to subsequent viral infection. To study this, we prepared RNA from whole lung homogenate of mouse lungs undergoing respiratory infection (IAV). For experiment (1), we compared mice undergoing either primary infection or secondary infection. Mice undergoing primary infection are defined as naive mice that are seeing IAV (PR8) for the first time. For secondary infection, we primed mice by infection of one strain of IAV (X31), waited 5 weeks for recovery, and then infected them with PR8 at the same time as mice undergoing primary infection. Lungs were harvested at days 1, 2, and 3 post-infection. Uninfected mice at baseline were also prepared as controls. For experiment (2), we wanted to determine the effects of IL-10 signaling in secondary infections. For these, we prepared memory mice as previously described, and then simultaneously administed an IL-10R blocking antibody at the time of infection. Lungs were collected at 2 days post infection, and uninfected mice were used as control.

first: Alexander

middle: Y

last: Yang


title: Characterization of induced cohesin loop extrusion trajectories in living cells [Hi-C]

status: Public on Jun 26 2025

city: Utrecht

first: Peter

last: Krijger

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: The cohesin complex shapes chromosomes by DNA loop extrusion, but individual extrusion trajectories were so far unappreciable in vivo. Here, we developed and validated TArgeted Cohesin Loader (TACL), a system enabling the strong activation of anchored loop extrusion from dozens of defined genomic sites in living cells. Studying their individual loop extrusion trajectories revealed that extruding cohesin-STAG2 stops not only at domain boundaries but at all flanking CTCF sites, engaging them in a complex transient looping network that supports intradomain contacts. Cohesin-STAG1 cannot associate with weak CTCF binding sites and fails to similarly support intradomain interactions. NIPBL-MAU2 remains associated with cohesin when stalled at looping CTCF sites, suggesting these factors may also be required for loop stabilization. TACL induces cohesin traffic jams and illegal loops with divergent CTCF sites, demonstrating that stalled cohesin can block extruding cohesin in vivo. Genes exposed to TACL-induced loop extrusion were collectively hindered in transcription and the underlying chromatin altered its accessibility and reduced its H3K27ac marks. Thus, by enabling the study of individual loop extrusion trajectories in vivo, we could assign new functions to players, identify new looping networks and uncover an interplay between loop extrusion, gene transcription and chromatin composition.

overall_design: HiC-contact profiles of eHAP1 cells carrying 27 TetO platforms expressing TetR-MAU2 (TACL) treated with or without doxycycline for 1 hour or TetR-mCherry.

first: Ruiqi

last: Han

first: Yike

last: Huang

last: Robers

first: Mikhail

last: Magnitov

first: Iwan

last: Vaandrager

first: Amin

last: Allahyar

first: Marjon

last: Verstegen

first: Kexin

last: Zhang

first: Elzo

last: de Wit

first: Wouter

last: de Laat


title: Characterization of induced cohesin loop extrusion trajectories in living cells [BrU-seq]

overall_design: ChIPseq  of eHAP1 cells carying 27 TetO platforms expressing TetR-MAU2 (TACL) or TetR-mCherry, with and without doxycycline treatment and/or depletion of RAD21, CTCF, PDS5A, WAPL, STAG2  using auxin treatment.


title: Characterization of induced cohesin loop extrusion trajectories in living cells [4C-seq]

overall_design: 4C-seq  of eHAP1 cells carying 27 TetO platforms expressing TetR-MAU2 (TACL) or TetR-mCherry, with and without doxycycline treatment and/or depletion of RAD21, CTCF, PDS5A, WAPL, STAG2  using auxin treatment.


title: Characterization of induced cohesin loop extrusion trajectories in living cells  [ATAC-seq]


title: Characterization of induced cohesin loop extrusion trajectories in living cells

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

overall_design: Refer to individual Series


title: BICC1 is a genetic modifier for Polycystic Kidney Disease

status: Public on Jun 28 2025

city: Cleveland

first: Oliver

last: Wessely

state: OH

address: 9500 Euclid Avenue/NC10

department: Cardiovascular and Metabolic Sciences

institute: Cleveland Clinic Foundation

summary: Autosomal dominant polycystic kidney disease (ADPKD) is primarily of adult-onset and caused by pathogenic variants in PKD1 or PKD2. Variable disease expression is incompletely understood with rare very early-onset PKD (VEO-PKD) presentations in utero or infancy. In animal models, the RNA-binding molecule Bicc1 has been shown to play a crucial role in the pathogenesis of PKD. To further investigate this, we first demonstrated that BICC1 physically binds to the proteins Polycystin-1 and -2 encoded by PKD1 and PKD2 via distinct protein domains. Furthermore, PKD was aggravated in loss-of-function studies in Xenopus and mice. These resulted in more severe disease when Bicc1 was depleted in conjunction with Pkd1, Pkd2 or Pkhd1., Finally, in a large human patient cohort, we identified several VEO-PKD patients that exhibited compound situations of PKD1, PKD2 and PKHD1 in conjunction with BICC1 as well as a sibling pair with a homozygous BICC1 mutation. Together these findings support the hypothesis that BICC1 cooperates with PKD1 and PKD2, and that BICC1 variants may aggravate disease severity highlighting RNA metabolism as an important new concept for disease modification in ADPKD.

overall_design: HEK cells were edited using CRISPR/Cas9 to knockout BICC1 or introduce a point mutation in S240P. Cells were grown under standard conditions and processed for RNA extraction and bulk mRNA sequencing.

first: Uyen

last: Tran

first: Lahoucine

last: Izem

first: R

last: Schweickart


title: Gene expression profile at single cell level for human metastatic melanoma samples

status: Public on Jun 24 2025

city: Piscataway

first: Jiekun

address: 145 Bevier Rd

institute: Rutgers University

summary: There exists great intra- and inter-tumor heterogeneity for metastatic melanomas. We used single cell RNA sequencing (scRNA-seq) to analyze cell type heterogeneity of metastatic melanoma and cell type specific responses to different treatments.

overall_design: We enzymatically digested and dissociated fresh tumor samples and analyzed using scRNA-seq.

first: Genevieve

last: Boland

first: Manolis

last: Kellis