title: CDK12/13 inhibition in NSCLC cell lines with acquired resistance to sotorasib

city: Tampa

first: Eric

last: Haura

state: FL

address: 12902 Magnolia Drive

institute: H. Lee Moffitt Cancer Center and Research Institute, Inc

summary: The efficacy of KRAS-G12C inhibitors in lung cancer is limited by the rapid onset of acquired resistance. While divergent mechanisms of resistance across patients and preclinical models have complicated efforts to identify therapeutic strategies for sotorasib-resistant cancers, we found that sotorasib-resistant H358 and LU65 cell lines, which have distinct mechanisms of resistance and drug sensitivity profiles, both exhibited increased vulnerability to treatment with SR-4835, an inhibitor of the transcriptional kinases CDK12 and CDK13. To identify CDK12/13-dependent genes linked to the increased sensitivity we observed in sotorasib-resistant over parental cells, we treated parental and sotorasib-resistant H358 and LU65 cells with SR-4835 and performed RNA sequencing.

overall_design: Whole-transcriptome RNA sequencing was performed in three independent biological replicates of parental and sotorasib-resistant H358 and LU65 cell lines after 24-hour treatment with 0.1% DMSO or 100 nM SR-4835.

first: Yaakov

last: Stern

first: Andrii

last: Monastyrskyi

first: Derek

last: Duckett


title: Activated Glucocorticoid Receptor is an Estrogen Receptor Silencer in ERα+ metastatic breast cancer.

status: Public on Oct 15 2025

city: Basel

first: Mohamed

last: Bentires-Alj

address: Hebelstrasse 20

department: DBM

country: Switzerland

institute: University Hospital Basel

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.

overall_design: Refer to individual Series


title: The Function of Tetrameric MADS-box Transcription Factors in Floral Fate Determination

status: Public on Oct 06 2025

city: Berlin

first: Manuel

last: Neumann

address: Philippstr. 13

country: Germany

institute: HU Berlin

first: Xiaocai

last: Xu

first: Frederic

last: Carew

first: Cezary

last: Smaczniak

first: Kerstin

last: Kaufmann


title: Injury and Therapy in a Human Spinal Cord Organoid [scRNA-seq]

status: Public on Oct 03 2025

city: Chicago

first: NOZOMU

last: TAKATA

state: Illinois

address: 303 East Superior Street, 10-220

department: Center for Vascular and Developmental Biology

country: USA

institute: Northwestern University Feinberg School of Medicine

summary: Damage of the spinal cord, which can lead to irreversible paralysis and loss of sensory function, is among the most devastating injuries suffered by humans. A significant effort has been made over the past few decades to find potential therapies to treat spinal cord injury (SCI), an objective that faces the challenge of central nervous system regeneration. Experimental access to human spinal cord tissue is therefore a critical need for discovery of SCI therapies and thus availability of the organ mimics known as organoids offers great potential. Research on spinal cord organoids has been sparse and only very recently enabled by the discovery of the necessary human progenitor cells derived from pluripotent stem cells. We report here on a human organoid model to simulate SCI in vitro and test the potential of novel therapies. We found that the model, involving injury of the organoid with a sharp scalpel, reveals immediate neuronal death and subsequently generates the characteristic glial scar observed after injury with its biological markers. Exposure of the injured organoid to a recently discovered pre-clinical therapy for SCI avoids formation of the scar and promotes axon regeneration in the area of the lesion. Furthermore, in the absence of injury we directly observed the activation of the developmental program to extend axons by the tested therapy, which contains bioactive nanofibers with intense supramolecular motion. The model developed here could accelerate discovery of therapeutic strategies to treat the broad spectrum of spinal cord injuries.

overall_design: Comparative gene expression profiling analysis of single cell RNA-seq data for human spinal cord organoids at two stages (5 weeks and 14 weeks in culture).

first: Nozomu

last: Takata

first: Ching

middle: M

last: Wai


title: Transcriptomic profiling of lung alveolar macrophages reveals distinct contribution of sterol metabolism in macrophage response to Cryptococcus gattii infection

status: Public on Oct 05 2025

city: klong luang

first: Siranart

last: Jeerawattanawart

state: Not US or Canada

address: 99 Moo 18, Paholyothin Road

department: Department of Medical Technology,Faculty of Allied Health Sciences

country: Thailand

institute: Thammasat University

summary: Alveolar macrophages are key first responders to pulmonary cryptococcosis, but there is still limited knowledge on the dynamic molecular changes during Cryptococcus gattii infection. We therefore analyzed the transcriptional profiles of alveolar macrophages isolated from mice infected intranasally with C. gattii and compared those infected with C. neoformans or treated with PBS at 7 days postinfection, using RNA sequencing. In C. gattii-infected mice, alveolar macrophages displayed the alteration of gene expression linked to sterol biosynthesis, while macrophages from C. neoformans-infected mice were primarily associated with interferon and cytokine signaling pathways. Thus, our research revealed the distinct patterns in the alveolar macrophage response to C. gattii infection.

overall_design:
To investigate the transcriptional characteristics of alveolar macrophages isolated from mice intranasally infected with C. gattii R265 using RNA sequencing analysis. A pairwise comparison of DEGs was carried out, which included (1) AMs of the PBS-treated mice (submitted to GEO previously as GSM6597668) compared with those of the C. gattii R265-infected mice at 7 days after infection and (2) AMs of the C. neoformans H99-infected mice (submitted to GEO previously as GSM6597669) compared with those of the C. gattii R265-infected mice at 7 days after infection.

***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.
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first: Adithap

last: Hansakon

first: Rudi

last: Alberts

first: Yongliang

last: Zhang

first: Pornpimon

last: Angkasekwinai


title: MS2-affinity purification coupled with RNA sequencing (MAPS) reveals S. aureus IsrR sRNA targetome

status: Public on Oct 02 2025

city: STRASBOURG

first: David

last: Lalaouna

address: 2, Allée Konrad Roentgen

department: Institut de Biologie Moléculaire et Cellulaire

country: France

institute: CNRS

summary: Bacterial regulatory RNAs (sRNAs) are commonly short non-coding RNAs that function as pleiotropic regulators by post-transcriptionally impacting mRNA stability and/or translation. They play significant roles in bacterial physiology and are typically expressed in response to specific environmental stimuli such as nutrient limitation. The bacterial pathogen Staphylococcus aureus faces decreased access to essential metal ions, including iron, in the mammalian host in a process called nutritional immunity. In response to host-mediated iron limitation, S. aureus expresses the sRNA IsrR, which coordinates an iron-sparing response by downregulating the expression of mRNAs coding for iron-requiring proteins. Herein, we utilized MS2-Affinity Purification coupled with RNA Sequencing (MAPS) to reveal the in vivo IsrR interaction network. Analysis of co-purified RNAs revealed previously unpredicted putative IsrR targets coding for proteins associated with iron-requiring processes. We validated that IsrR directly interacts with eight of these targets in vitro. We demonstrate physiological roles for IsrR in mediating heme biosynthesis, aerobic respiration, and the metabolism of oxygen radicals. These activities are critical for pathogenesis, and this study establishes how S. aureus leverages these processes to adapt to iron scarcity, which is commonly encountered in the mammalian host.

overall_design: Affinity purification of in vivo regulatory complexes coupled with high throughput RNA sequencing methodology or MAPS, which stands for “MS2 affinity purification coupled with RNA". MS2-IsrR was used as a bait.


title: Hypoxia promotes airway differentiation in the human lung epithelium  [scRNAseq_hypoxia_AT2]

city: Cambridge

first: Emma

last: Rawlins

address: Tennis court road

country: United Kingdom

institute: University of Cambridge

summary: Human early embryos develop under physiological hypoxia, but how hypoxia regulates human lung organogenesis remains little known. We have investigated oxygen availability effects on the human lung epithelium using organoids. We find first-trimester lung epithelial progenitors remain undifferentiated under normoxia, but spontaneously differentiate towards multiple airway cell types and inhibit alveolar differentiation under hypoxia. Using chemical and genetic tools, we demonstrate that hypoxia-induced airway differentiation is dependent on HIF (Hypoxia-Inducible Factor) pathways, with HIF1α and HIF2α differentially regulating fate decisions. Transcription factors KLF4 and KLF5 are direct targets of the HIF pathway and promote progenitor differentiation to basal and secretory cells. Chronic hypoxia also reprogrammed human alveolar type 2 cells to airway cells via the HIF pathway. Our results reveal roles for hypoxia and HIF signalling during human lung development and have implications for aberrant cell fate decisions in chronic lung diseases.

overall_design: Time series single cell RNA-seq of human fetal lung-derived AT2 (fdAT2) cells isolated from one donor cultured under hypoxia for 0, 6, 15, 30 days, and back to normoxia for 6, 15, 30 days. The two sub-libraries were prepared with Evercode Whole Transcriptome v3 mini kit. Each sublibrary is a mixture of all 7 barcoded samples (7 time points). Sample loading information is attached for demultiplexing.

first: Ziqi

last: Dong


title: Injury and Therapy in a Human Spinal Cord Organoid II [scRNA-seq]

overall_design: Comparative gene expression profiling analysis of single cell RNA-seq data for human spinal cord organoids at two stages (20 weeks and 28 weeks in culture).


title: RNA sequencing of Tcf7 and Prdm1 deficient T cells [RNAseq_Tcf7Prdm1DKO]

city: SAINT LOUIS

first: Takeshi

last: Egawa

state: MO

address: 660 S. Euclid Ave

department: Pathology and Immunology

institute: Washington University in St. Louis

summary: The transcription factors Tcf7 (encoding TCF1) and Prdm1 (encoding Blimp1) exhibit opposing effects on T cell differentiation. While TCF1 promotes the maintenance of T progenitor exhausted cells, Blimp1 drives their differentiation into terminally exhausted effector cells. However, the impact of the combined deletion of these factors on CD8 T cell differentiation remains to be defined. We found that CD8 T cells in which TCF1 and Blimp1 are both ablated exhibit a TPEX surface phenotype in chronic infection but fail to expand in recall settings. To better understand how these factors poise T cells to respond to antigen encounter, bulk RNA-sequencing was performed on TPEX cells from WT and Tcf7 Prdm1 DKO CD8 T cells.

overall_design: The dataset consists of RNA-seq samples collected from biological replicates of four WT and four Tcf7 Prdm1 DKO mice. PD1+SLAMF6+TIM3- CD8+ T cells were isolated 21 dpi with LCMV-c13.

first: Maegan

last: Murphy


title: Prdm1-creER fate maps cells with memory and effector potential [RNAseq_Prdm1tdt]

summary: The transcription factor Blimp1 (encoded by Prdm1) is upregulated in CD8+ T cells early in responses to viral infection. The role of Blimp1 in promoting effector differentiation suggests that it may enforce commitment of cells to an effector fate. However, the target genes that Blimp1 regulates to promote effector differentiation remain incompletely defined. To examine genes associated with Prdm1 induction early in an immune response, we sorted Prdm1-creERT2 fate mapped and non-fate mapped cells on 6 days post LCMV-Arm infection after fate mapping on 3 and 4 days post infection.

overall_design: Prdm1-creER R26-lsl-tdTomato P14 TCR transgenic T cells were transferred into congenic recipient mice, which were infected with LCMV-Arm one day post transfer. Tamoxifen was administered by oral gavage on 3 and 4 days post infection. On day 6 post-infection, memory-biased KLRG1+ and effector-biased KLRG1- cells were sorted, with tdTomato + and tdTomato- cells being separated into distinct tubes for each population. Biological duplicates were sorted for each sample.


title: Injury and Therapy in a Human Spinal Cord Organoid [RNA-seq]

summary: Damage to the spinal cord, which can lead to irreversible paralysis and loss of sensory function, is among the most devastating injuries suffered by humans. A significant effort has been made over the past few decades to find therapies to treat spinal cord injury (SCI) but translation of pre-clinical work remains elusive. Experimental access to human spinal cord tissue is therefore critical to accelerate discovery of effective SCI therapies. Thus, availability of the organ mimics known as organoids offers great potential for this important objective. We report here on the development of two human organoid injury models to simulate SCI in vitro, using as a therapy bioactive supramolecular assemblies of peptide amphiphiles. The system tested here has been recently shown to be highly effective at reversing paralysis in an acute murine model following severe SCI. The models use either a laceration of the organoid with a scalpel or a compressive contusion commonly used in preclinical models. We found that both injuries result in immediate neuronal death and interestingly generate glial scar-like tissue. Exposure of the injured organoids to the pre-clinical therapy validated in vivo avoided formation of the scar-like tissue and promoted significant axonal regeneration. Furthermore, in the absence of injury, we directly observed the activation of the developmental program that extends neurites as a result of the therapy. Our observations indicate that injury models on human organoids could accelerate the discovery of therapies to treat spinal cord injury and possibly damage of other central nervous system tissues due to trauma or disease.

overall_design: Comparative gene expression profiling analysis of injured organoids and therapy treatment

first: Matthew

last: Schipma


title: Epigenetic characterization of T progenitor exhausted and terminally exhausted T cells in chronic infection [ATACseq_Prdm1YFP]

summary: Exhausted T cells are a heterogeneous population of antigen-reactive CD8+ T cells elicited by chronic antigen exposure. T progenitor exhausted (TPEX) and terminally exhausted (TEX) cells exhibit distinct gene expression profiles, but how their chromatin accessibility profiles differ remains incompletely defined. This dataset interrogates genome-wide differences in chromatin accessibility of Prdm1YFP+TIM3+ (TEX), Prdm1YFP-TIM3-(TPEX), and Prdm1YFP+TIM3- cells.

overall_design: Prdm1-YFP+ reporter mice were infected with LCMV-c13; on 22 dpi, PD1+CD8+ T cells from the following populations were sorted: Prdm1YFP+TIM3+ (TEX), Prdm1YFP-TIM3-(TPEX), and Prdm1YFP+TIM3-. Three independent mice were used for each sample. Bulk ATAC sequencing was performed on each replicate.

first: Saravanan

last: Raju


title: ATAC sequencing of Tcf7 and Prdm1 deficient T cells [ATACseq_Tcf7Prdm1DKO]

summary: The transcription factors Tcf7 (encoding TCF1) and Prdm1 (encoding Blimp1) exhibit opposing effects on T cell differentiation. While TCF1 promotes the maintenance of T progenitor exhausted cells, Blimp1 drives their differentiation into terminally exhausted effector cells. However, the impact of the combined deletion of these factors on CD8 T cell differentiation remains to be defined. We found that CD8 T cells in which TCF1 and Blimp1 are both ablated exhibit a TPEX surface phenotype in chronic infection but fail to expand in recall settings. To better understand how these factors poise T cells to respond to antigen encounter, bulk ATAC-sequencing was performed on TPEX cells from individual and combined transcription factor deficient CD8 T cells.

overall_design: The dataset consists of ATAC samples collected from biological replicates of three WT, two Prdm1 KO, one Tcf7 KO, and three DKO mice. PD1+SLAMF6+TIM3- CD8+ T cells were isolated 21 dpi with LCMV-c13.

first: Joshua

last: Deffenbaugh


title: Comprehensive Identification and Functional Analysis of Fully Disordered Proteins Essential for Cell Survival

status: Public on Sep 30 2025

city: Bunkyo-ku

first: Tatsuya

last: Ishizuka

state: Tokyo

address: 1-1-1 Yayoi

department: Institute for Quantitative Biosciences

country: Japan

institute: The University of Tokyo

summary: Proteins have traditionally been understood through their tertiary structures, with well-defined conformations considered essential for biological function. This classical structure-function paradigm implies that proteins with high intrinsic disorder would be less critical for cellular survival. However, recent discoveries have suggested that some intrinsically disordered proteins or even fully disordered proteins without any apparent tertiary structures are essential. Nevertheless, the biological significance of such disordered proteins is not comprehensively understood. Here, using genome-wide CRISPR screening, we demonstrated that highly or fully disordered proteins show comparable essentiality to well-folded proteins. Although structured proteins are more prevalent among essential genes, we found that the proportion of essential proteins is comparable across proteins of varying disorder levels. Focusing on FAM32A, one of the essential, fully disordered proteins identified in our screen, we show that its depletion leads to increased intron retention and downregulation of many other essential genes. These findings reshape our understanding of the structure-function paradigm, highlighting that fully disordered proteins can be essential for cellular viability.

overall_design: RNA-seq profiles of wildtype HEK293T cells and their knockdown derivatives by siFAM32A, 24 hours after transfection. Total RNA and fractionated nuclear and cytoplasmic RNA samples were sequenced.

first: Kotaro

last: Tsuboyama

first: Yukihide

last: Tomari


title: HPV vaccines with different adjuvant types for NHP

city: Rahway

first: Yuhyun

last: Ji

state: NJ

address: 126 E Lincoln Ave

institute: Merck & Co., Inc.

summary: Adjuvants can differentially shape the immune response when included in vaccines, and their effects depend on multiple variables. To investigate how different adjuvant classes influence immune signaling, we performed RNA-seq analysis on nonhuman primates (NHPs).

overall_design: Peripheral blood was collected from rhesus macaques at baseline, 1 day, and 7 days after each vaccine dose to profile transcriptional responses to different adjuvants. Total RNA was isolated from whole blood preserved in PAXgene tubes using the PAXgene Blood RNA kit, with RNA quality and quantity assessed on an Agilent Bioanalyzer. Cell pellets were washed and lysed according to sample type, and RNA extractions were performed using standard methods to preserve high RNA integrity. Strand-specific RNA-seq libraries were prepared with the TruSeq Stranded Total RNA Ribo-Zero kit, which depletes ribosomal RNA and retains both coding and noncoding transcripts. Libraries were sequenced on an Illumina platform using paired-end 50 bp reads, with sequencing depth and multiplexing set to achieve adequate coverage for downstream analyses. Reads were processed and mapped to reference annotations, and orthologues were identified via Ensembl BioMart for cross-species gene comparisons. The resulting gene expression matrices were used to compare adjuvant-dependent changes in immune gene expression across time points.


title: Impact of TCF-1 de-repression on effector gene expression programs [RNAseq_Tcf7del22+17]

summary: The transcription factor TCF-1 is downregulated during effector differentiation of CD8+ T cells. However, how its downregulation impacts gene expression in different effector- and memory-biased populations remains unclear. Here, we generate mice in which TCF-1 fails to become downregulated in differentiated effector cells and probe the transcriptional impact of TCF-1 retention in different T cell differentiation states bybulk RNA-sequencing of KLRG1+ effector T cells.

overall_design: RNA-sequencing of WT + Cd19 RNP control P14 TCR trangenic cells and Tcf7∆22kb + Tcf7+17kb RNP P14 TCR transgenic cells isolated on 8 days post infection with LCMV-Armstrong.


title: Transcriptomic analysis of Hela Ezrin inhibited cells

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

summary: Ezrin (EZR), a cell membrane to cytoskeleton linker protein,  plays key roles in maintaining cellular homeostasis. Its deregulation at various levels strongly correlates with cancer progression, metastasis and higher patient mortality.  However, the precise mechanistic basis for its role remains unknown. Recently, we demonstrated that Ezrin participates in EGFR/AKT signaling pathways. Importantly, transitions between active (phosphorylated open) and inactive (dephosphorylated closed) forms of Ezrin is crucial for its function in cancer. Gene expression analysis suggested dysregulation of genes that are functionally linked to cell energetic metabolism with potential implications for cell proliferation, survival and apoptosis. Total RNA was extracted from n=4 for each experimantal group: Transcriptomic analysis was performed on HeLa DMSO and Ezrin inhibitor-treated cells.

first: Ivan

last: Conte

first: Giuliana

last: Giamundo


title: Expression profiling of the human bone marrow niche remodeling in clonal hematopoiesis and myelodysplasia [exhaustion]

status: Public on Sep 29 2025

first: Judith

last: Zaugg

department: Departement Biomedizin

institute: University of Basel

summary: Somatic mutations in hematopoietic stem/progenitor cells (HSPCs) can lead to clonal hematopoiesis of indeterminate potential (CHIP) and progression to myelodysplastic syndromes (MDS). Using single-cell and anatomical profiling of a large cohort of human bone marrow (BM), we show that the HSPC BM niche in CHIP and MDS is undergoing inflammatory remodeling. This includes loss of CXCL12⁺ adipogenic stromal cells and the emergence of a distinct population of inflammatory mesenchymal stromal cells (iMSCs), which arise in CHIP and become more prevalent in MDS. Functional studies in primary BM HSPC-MSC co-cultures reveals that healthy aged and CHIP HSPCs activate stromal support, while MDS HSPCs fail to do so. In contrast, MDS blasts further suppress HSPC support and trigger inflammation, indicating disease-stage-specific stromal disruption. In parallel, we show that iMSCs retain partial support and angiogenic potential in MDS, coinciding with expanded BM vasculature. Additionally, we identify IFN-responsive T cells that preferentially interact with iMSCs, potentially reinforcing local inflammation. These findings position iMSCs as central mediators of early BM niche dysfunction and potential therapeutic targets for intercepting pre-malignant hematopoiesis.

overall_design: 36 whole BM aspirates (12 MDS patients, 12 CHIP donors, and 12 age-matched controls), curated as part of the BoHemE study (NCT02867085), were used for NanoString analysis.

first: Karin

middle: D

last: Prummel

first: Kevin

last: Woods

first: Maksim

last: Kholmatov

first: Eric

middle: C

last: Schmitt

first: Evi

middle: P

last: Vlachou

first: Mayssa

last: Labyadh

first: Rebekka

last: Wehner

first: Gereon

last: Poschmann

first: Kai

last: Stühler

first: Susann

last: Winter

first: Uta

last: Oelschlaegel

first: Manja

last: Wobus

first: Logan

middle: S

last: Schwartz

first: Pedro

middle: L

last: Moura

first: Eva

last: Hellström-Lindberg

first: Krishnaraj

last: Rajalingam

first: Matthias

last: Theobald

first: Jennifer

middle: J

last: Trowbridge

first: Clémence

last: Carron

first: Thierry

last: Jaffredo

first: Marc

last: Schmitz

first: Uwe

last: Platzbecker

middle: B

first: Borhane

last: Guezguez


title: Single-cell profiling of the human bone marrow niche remodeling in clonal hematopoiesis and myelodysplasia

first: Judith

last: Zaugg

overall_design: Non-hematopoietic stromal fraction, HSPCs and T cells isolated using FACS were analysed with scRNA-seq.

first: Karin

last: Prummel

first: Kevin

last: Woods

first: Maksim

last: Kholmatov

first: Eric

last: Schmitt

first: Evi

last: Vlachou

first: Mayssa

last: Labyadh

first: Rebekka

last: Wehner


title: Single-cell profiling of the human bone marrow stromal cells in clonal hematopoiesis and myelodysplasia

overall_design: Stromal cells isolated using FACS were analysed with scRNA-seq.

first: Gereon

last: Poschmann

first: Kai

last: Stühler

first: Susann

last: Winter

first: Uta

last: Oelschlaegel

first: Manja

last: Wobus

first: Logan

last: Schwartz

first: Pedro

last: Moura

first: Eva

last: Hellström-Lindberg


title: Modeling in vivo induction of gastric insulin-secreting cells using transplanted human stomach organoids

status: Public on Sep 26 2025

city: New York

first: David

last: Redmond

state: New York

address: 1300 York Avenue

institute: Weill Cornell Medicine

summary: Insulin-dependent diabetes could be treated by supplying patients with primary pancreatic islets or other types of insulin-secreting cells. Functional insulin+ cells can be induced in situ from the murine stomach using defined genetic factors, offering a potential method to directly produce autologous insulin+ cells. Here, we modeled whether such gastric insulin-secreting (GINS) cells could be generated in vivo from human stomach tissues. We produced human gastric organoids (hGOs) from human embryonic stem cells engineered with inducible expression of reprogramming factors. The hGOs were stably transplanted for 6 months and showed robust cytodifferentiation resembling the human stomach in structure and cellular composition. Upon hGO maturation in vivo, we activated the reprogramming factors and observed formation of insulin+ cells, which secreted insulin into the circulation and ameliorated experimental diabetes. Our modeling indicates that GINS cells can be induced from human stomach tissues in vivo, warranting further therapeutic development for this technology.

overall_design: This study aimed at providing insights into the cell identities of human gastric organoids overexpressing NPM factors. Single-cell RNA sequencing was employed to analyze the transcriptomes of ECAD+ epithelial cells from human gastric organoids treated for 10 days with doxycycline.

first: Jiaqi

last: Lu

first: Capucine

last: Martin

first: Xiaofeng

last: Huang

first: Hyunkee

last: Kim


title: Expression profiling of the human bone marrow niche remodeling in clonal hematopoiesis and myelodysplasia [PanCancer]

first: Judith

last: Zaugg

first: Karin

last: Prummel

first: Kevin

last: Woods

first: Maksim

last: Kholmatov

first: Eric

last: Schmitt

first: Krishnaraj

last: Rajalingam

first: Matthias

last: Theobald

first: Jennifer

last: Trowbridge

first: Clémence

last: Carron

first: Thierry

last: Jaffredo

first: Marc

last: Schmitz

first: Uwe

last: Platzbecker

first: Borhane

last: Guezguez


title: Influenza NS1 Drives N6-Methyladenosine (m6A)-Mediated Autoregulation of Viral mRNA Splicing

status: Public on Sep 24 2025

city: Hong Kong

first: Honglin

last: Chen

state: Hong Kong

address: L501, 5/F, Lab Block, 21 Sassoon Road, Pokfulam, HK

department: Microbiology

country: Hong Kong

institute: The University of Hong Kong

summary: Influenza A virus replication requires precise balance between unspliced and spliced viral mRNAs. However, the regulatory mechanisms governing viral mRNA splicing remain poorly understood. In this study, we uncover an epigenetic strategy whereby the viral NS1 protein autoregulates its own mRNA splicing via N6-methyladenosine (m6A) modification. Specifically, m6A modification at residue A385 on NS mRNA recruits the m6A reader YTHDC1, which competitively inhibits the splicing factor SRSF3 from binding proximal sites. Importantly, we demonstrate that the A385 m6A site is conserved and essential for splicing regulation in the NS segment across human and avian influenza strains. Our findings suggest that, by dynamically modulating m6A levels, NS1 fine-tunes viral mRNA processing to enhance replication efficiency. This work elucidates NS1 as an m6A-driven splicing regulator and identifies this conserved m6A site as a potential target for broad-spectrum antiviral development.

overall_design: A549 cells were infected by A/WSN/1933 (H1N1) (WSN) viruses for three biological replicates. Samples were collected in 3 and 9 hours post infection for Direct sequencing analysis.

first: Yingyin

last: Liao

first: Bobo Wing-Yee

last: Mok


title: A transcriptomic cell atlas of the developing Brachypodium leaf at single-cell resolution

status: Public on Sep 23 2025

city: BERN

first: Michael

middle: T

last: Raissig

address: Altenbergrain 21

department: Institute of Plant Sciences

institute: University of Bern

summary: We employed scRNA-seq to generate a cell atlas of the early leaf development in the wild model grass Brachypodium distachyon.

overall_design: Samples were collected from 15 leaf developmental zones (per dataset) (2021, 2022 and 2024 datasets) and 8 or 10 vegetative shoot apices with young leaf primordia (2023 datasets) of 3 weeks old soil-grown plants. Two genotypes were harvested: Wild type Bd21-3 (WT) and the sid/bdmute-1 (sid) mutant. The tissue was digested to release single cells (protoplasts) which were then sent for 10X Genomics single-cell sequencing. The 2022 libraries were sequenced twice (indicated by -1 and -2).

first: Lea

last: Berg

first: Inés

last: Hidalgo Prados


title: Transcriptional responses to protoplasting in the early leaf developmental zone of Brachypodium distachyon

summary: We employed bulk RNA-seq to find protoplasting-induced genes in the wild model grass Brachypodium distachyon.

overall_design: Samples were collected from leaf developmental zones of 3 weeks old Brachypodium distachyon Bd21-3. 10 leaf developmental zones were digested to release single cells (protoplasted) and 5 leaf developmental zones were used for the non-protoplasted samples. Three replicates were produced per treatment. Total RNA extraction, poly-A-based library preparation and bulk-RNA sequencing of these samples allowed to check for genes that are affected by protoplasting.

first: Ambuj

last: Gore


title: Endothelial RNF20 Suppresses Endothelial-to-Mesenchymal Transition and Safeguards Physiological Angiocrine Signaling to Prevent Congenital Heart Disease

city: Mannheim

first: Gergana

last: Dobreva

state: Baden Württemberg

address: Ludolf-Krehl-Str. 7-11

department: Cardiovascular Genomics and Epigenomics

institute: Medical Faculty Mannheim/University of Heidelberg

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

overall_design: Refer to individual Series

first: Julio

last: Cordero Henriquez

first: Yianliang

last: Dou


title: DNA methylation changes during prostate cancer lineage transitions

status: Public on Sep 22 2025

city: Seattle

first: Brian

last: Hanratty

state: WA

address: 1100 Fairview Avenue

department: Division of Human Biology

institute: Fred Hutchinson Cancer Cancer

type: Methylation profiling by high throughput sequencing

summary: Conversion to a neuroendocrine phenotype is a known resistance mechanism to androgen receptor-directed therapies in prostate cancer. In this study, we analyze DNA methylation changes associated with neuroendocrine transdifferentiation using a patient-derived xenograft model that recapitulates these lineage transitions.

overall_design: DNA samples from the LTL331 patient-derived xenograft model, developed by Dr. Wang (Vancouver Prostate Centre, PMID: 24356420), were collected at various time points post-castration and analyzed using enzymatic DNA methylation sequencing (EM-seq, PMID: 34140313).

last: Haffner

first: Yuzhuo

last: Wang

first: Mohamed

last: Adil


title: Peripheral Regulatory T Cells in Major Depressive Disorder Exhibit a Th1-like Feature with Compromised Suppressive Function

status: Public on Sep 20 2025

city: xi'an

first: Yao

last: Gao

address: 277 Yanta West Road

department: Psychiatry

country: China

institute: the first affiliated hospital of Xi'an Jiaotong University

summary:
Background: Major depressive disorder (MDD) is pathologically linked to inflammatory-immune dysregulation. Although regulatory T cells (Tregs) are crucial for immune homeostasis, clinical studies have demonstrated a paradoxical dynamic (deficiency vs. expansion) feature of peripheral Tregs in patients with MDD. However, disease-specific plasticity and microenvironmental reprogramming mechanisms remain elusive, highlighting the need for pathology-driven biomarkers and targeted therapies.
Methods: We integrated mass cytometry (CyTOF; n=37), single-cell RNA/T cell receptor sequencing (n=10), and flow cytometry (n=123) to profile Tregs in MDD. Functional assays assessed the suppression capacity, interleukin (IL)-6/interferon (IFN)-γ-driven plasticity, and biomarker potential using a receiver-operating characteristic (ROC) analysis.
Results: Patients with MDD exhibited significant peripheral immune dysregulation, notably expanded peripheral Tregs (1.2-fold vs. controls, p=0.001). Single-cell analysis revealed that the expanded Tregs were mainly T-bet+ Th1-like subpopulations (1.5-fold vs. controls, p=0.01) with metabolic abnormalities, featuring mitochondrial dysfunction (reduced activity of the oxidative phosphorylation pathway, FDR<0.001) and abnormally high expression of IFN-γ (gene set enrichment score NES=2.55), along with a significant reduction in the immunosuppressive capacity (16.7% vs. 62.8% inhibition, p<0.001). Further investigation revealed that the IL-6 signaling pathway drove the abnormal differentiation of Th1-like Tregs, and IL-6 blockade reversed their inflammatory phenotype (1.8-fold reduction, p<0.001). Clinically, T-bet+ Th1-like Tregs distinguished drug-naïve MDD patients with high accuracy (AUC=0.776, 95% CI: 0.668-0.884), correlating with symptom severity (HAMD: r=0.49, p<0.001).
Conclusions: MDD-associated IL-6-driven Th1-like Treg polarization underpins MDD immunopathology, combining metabolic failure and inflammatory effector conversion. These cells serve as dual diagnostic biomarkers and therapeutic targets, supporting IL-6/IFN-γ axis modulation for depression treatment.

overall_design: After isolating peripheral blood mononuclear cells (PBMCs) from the peripheral blood of patients with MDD (n=6) and healthy controls (n=4), regulatory T cells (Treg cells) were separated from PBMCs by magnetic column sorting. Single-cell RNA and T-cell receptor (TCR) sequencing analyses were performed on the sorted Treg cells.

first: Zihan

last: Lei

first: Xianyan

last: Zhan

first: Yifan

last: Ren

first: Zirong

first: Qingyan

last: Ma

first: Wei

first: Yunpeng

first: Yijie

last: Guo

first: Yuan

first: Yan

last: Li

first: Feng

last: Zhu

first: Xiancang

first: Pan


title: Spatiotemporal dynamics of the cardioimmune niche during lesion repair [spatial]

city: Würzburg

first: Andy

middle: Shing Fung

last: Chan

address: Gebäude E6,, Versbacher Str. 9

institute: Institute for Systems Immunology, University of Würzburg

summary:
[Important Note: Some files appear to have become corrupted during upload, and we are currently replacing them, which may take a few working days. In the meantime, if you need access to the raw data files, please email shing-fung.chan@uni-wuerzburg.de. We apologize for the inconvenience.]

The heart is one of the least regenerative organs in humans, and heart disease is the leading cause of death worldwide. Understanding the cellular and molecular processes during cardiac wound healing is an essential prerequisite to reduce health burden and improve cardiac function after myocardial tissue damage. By integrating single-cell RNA-sequencing with imaging-based spatial transcriptomics, we reconstructed the spatiotemporal dynamics of the fibrotic niche after ventricular injury in adult mice. Our analysis revealed dynamic regulation of local cell communication niches over time. We identified interactions that regulate cardiac repair, including fibroblast proliferation silencing by Trem2high macrophages that prevents excessive fibrosis. Moreover, we discovered a rare population of dedifferentiating cardiomyocytes early post-lesioning repair, sustained by signals from myeloid and lymphoid cells. Culturing non-regenerative mouse cardiomyocytes or human heart tissue with these niche factors reactivated progenitor gene expression and cell cycle activity. In summary, this spatiotemporal cell type atlas offers valuable insights into the heterocellular interactions that control cardiac repair.

overall_design: Cryoablation of the left ventricle (Cryo) was used as the mouse models to introduce ventricular lesions. After recovery of animals from lesion induction, we isolate the LV. 5μm formalin-fixed paraffin-embedded tissue sections (transverse plane of the LV) were mounted on a Xenium slide within the desired imaging region.

first: Lisa

last: Marschhäuser

first: Wing

last: Cheung

first: Franziska

last: Schneider-Warme

first: Dominic

last: Grün


title: Evaluation of PFHpA impact on liver metabolism using human liver spheroids

status: Public on Sep 18 2025

city: Los Angeles

first: Ana

last: Maretti-Mira

state: CA

address: 1450 Biggy Street, NRT 3514

department: Medicine

institute: USC

summary: Accumulating evidence suggests that poly- and perfluoroalkyl substances (PFAS), a class of persistent organic pollutants, cause changes in hepatic lipid, amino acid, and glucose metabolism. Our study explores the molecular mechanisms whereby PFHpA disrupts liver metabolism and facilitate NAFLD development.

overall_design: 3D InSightTM human liver spheroids (InSphero) composed of hepatocytes (10 donors: 5 males and 5 females), endothelial cells, and macrophages (1 donor). Liver spheroids were maintained in low glucose medium (lean medium) were exposed to 20µM of PFHpA for 7 days. Control spheroids were cultured in lean medium for the same time. We dissociated spheroids with Trypsin, generating suitable cells for 10x genomics scRNAseq (kit 3’ v3.1).

first: A

first: M

last: Salomon

first: L

last: Golden-Mason


title: Spatiotemporal dynamics of the cardioimmune niche during lesion repair [scRNA-seq]

summary:
[Important Note: Some files appear to have become corrupted during upload, and we are currently replacing them, which may take a few working days. In the meantime, if you need access to the count matrix or metadata files, please email shing-fung.chan@uni-wuerzburg.de. We apologize for the inconvenience.]

The heart is one of the least regenerative organs in humans, and heart disease is the leading cause of death worldwide. Understanding the cellular and molecular processes during cardiac wound healing is an essential prerequisite to reduce health burden and improve cardiac function after myocardial tissue damage. By integrating single-cell RNA-sequencing with imaging-based spatial transcriptomics, we reconstructed the spatiotemporal dynamics of the fibrotic niche after ventricular injury in adult mice. Our analysis revealed dynamic regulation of local cell communication niches over time. We identified interactions that regulate cardiac repair, including fibroblast proliferation silencing by Trem2high macrophages that prevents excessive fibrosis. Moreover, we discovered a rare population of dedifferentiating cardiomyocytes early post-lesioning repair, sustained by signals from myeloid and lymphoid cells. Culturing non-regenerative mouse cardiomyocytes or human heart tissue with these niche factors reactivated progenitor gene expression and cell cycle activity. In summary, this spatiotemporal cell type atlas offers valuable insights into the heterocellular interactions that control cardiac repair.

overall_design: We utilized two common mouse models to introduce ventricular lesions: ligation of the left anterior descending coronary artery followed by reperfusion (LAD) and cryoablation of the left ventricle (Cryo). After recovery of animals from lesion induction, we isolate and vibratome-cut the LV into tissue slices of 300µm thickness. Slices had a radius of ~5mm, and the IZ (refers to day 1-7 of the wound)/ fibrotic zone (FZ, refers to day 28-56 of the repaired wound) was placed in the center surrounded by border zone (BZ) tissue. For scRNA-seq, CM and non-myocytes (NM) were isolated from cardiac slices obtained at 1, 3, 7, 28 and 56 days post-surgery. After CM exclusion, we combined unbiasedly-sorted samples with samples enriched for endothelial cells (EC), smooth muscle cells (SMC), pericytes and Schwann cells (SwC) (CD31+/CD146+), dendritic cells (CD45+CD14-CD11c+) and lymphocytes (CD45+CD14-CD11c-). In addition, we isolated DAPI+PCM-1+ nuclei for single-nucleus RNA-sequencing (snRNA-seq) of CM.

first: Joachim

last: Greiner

first: Tomas

last: Brennan

first: Eva

last: Rog-Zielinska

first: Peter

last: Kohl


title: Mapping disease-specific vascular cell populations responsible for obliterative arterial remodelling during the development of pulmonary arterial hypertension

status: Public on Sep 15 2025

city: Ottawa

first: Duncan

middle: J.

last: Stewart

state: Ontario

address: 501 Smyth Road

department: Regenerative Medicine

country: Canada

institute: Ottawa Hospital Research Institute

summary: Pulmonary arterial hypertension (PAH) is a lethal pulmonary vascular disease characterized by arteriolar pruning and occlusive vascular remodeling leading to increased pulmonary vascular resistance and eventually right heart failure. While endothelial cell (EC) injury and apoptosis are known triggers for this disease, the mechanisms by which they lead to complex arterial remodeling remain obscure. Aims: We employed multiplexed single-cell RNA sequencing at multiple timepoints during the onset and progression of disease in a model of severe PAH to identify mechanisms involved in the development of occlusive arterial lesions. Methods and Results: Single cell transcriptional analysis resolved 44 global lung cell populations, with widespread early transcriptomic changes at 1 week affecting endothelial, stromal and immune cell populations. In particular, two EC clusters were greatly expanded during PAH development and were identified as being disease specific: a relatively dedifferentiated (dD) EC population that was enriched for Cd74 expression while exhibiting a loss of endothelial identity; and an activated arterial EC (aAEC) population that uniquely exhibited persistent differential gene expression throughout PAH development consistent with a growth regulated state. dDECs were primed to undergo endothelial-mesenchymal transition as evidenced by reduced activity of master EC transcription factors, Erg and Fli1, and further supported by RNA velocity analysis showing vectors leading to fibroblast clusters. Of note, aAECs exhibited high expression of Tm4sf1, a gene implicated in cancer cell growth, that was also expressed by a smooth muscle (SM)-like pericyte cluster, and were highly localized to regions of arterial remodeling in both the rat model and PAH patients, contributing to intimal occlusive lesions and SM-like pericytes forming bands of medial muscularization. Conclusions: Together these findings implicate disease-specific vascular cells in PAH progression and suggest that TM4SF1 may be a novel therapeutic target for arterial remodeling. Translational Perspectives: Using single cell transcriptomic analysis in both human lung samples and a rat model of severe PAH we have identified disease-specific EC populations contributing to complex arterial remodeling, including growth-dysregulated, activated arterial ECs (aAECs) and dedifferentiated ECs (dDECs) that may be primed for endothelial to mesenchymal transition. In particular, aAECs exhibit high expression of a surface marker, TM4SF1, which is essential for their hyper-proliferative phenotype and represents a promising therapeutic target for RNA silencing approaches or as an antigen to guide immune-mediated ablation of this cancer-like EC population in PAH.

overall_design: Single cell RNA-seq profiling of PAH rat model with unique biological replicates at different time points on weeks 1, 3, 5, 8 and healthy. Data was later merged.

first: Nicholas

last: Cober

first: Emma

last: McCourt

first: Rafael

last: Godoy

first: Yupu

last: Deng

first: Ken

last: Schlosser

first: Elmira

last: Qamsari

first: Jalil

last: Azami

first: Elham

last: Salehisiavashani

first: David

last: Cook

first: Sarah-Eve

last: Lemay

first: Timothy

last: Klouda

first: Ke

last: Yuan

first: Sébastien

last: Bonnet


title: Transcriptional regulator SATB1 limits CD8 T cell population expansion and effector differentiation in chronic infection and cancer [RNA-Seq]

status: Public on Sep 12 2025

city: Melbourne

first: Lachlan

last: Dryburgh

state: Victoria

address: 792 Elizabeth Street

department: The Department of Microbiology and Immunology,  The University of Melbourne

country: Australia

institute: The Peter Doherty Institute for Infection and Immunity

summary: Gene expression profile of exhausted CD8+ T cell populations upon deletion of SATB1 in in chronic infection

overall_design: Naïve CD45.2+ SATB1-deficient P14 cells (Satb1flex/flex/Cd8Cre, SATB1-KO) or control cells (Satb1flex/flex) P14 cells were adoptively transferred into naïve wildtype CD45.1+ mice and subsequently infected with LCMV-Docile. On day 21 of infection, spleens were harvested. Single cell suspensions were prepared and cells enriched for CD8 T cells. The different populations were sorted. DNA libraries were constructed and sequenced


title: Inducible tag-free degradation of endogenous proteins with AlissAID and development of a photoactivable inducer

status: Public on Sep 11 2025

city: Chikusa-ku, Nagoya, Aichi

first: Kazuya

last: Ichihara

address: Furo-cho

institute: Nagoya University

summary: Protein analysis strategies involving targeted protein degradation are powerful approaches to determine gene functions. Auxin-inducible degron (AID) is among the most widely used methods for target protein knockdown. This system enables the rapid depletion of AID-tagged target proteins in an auxin-dependent manner. Various improved AID methods have been developed to date; however, the requirement to tag the target proteins remains a common challenge. Here, we demonstrated the efficiency of an affinity linker-based super-sensitive AID system for the conditional knockdown of target proteins in cultured animal cells and mouse embryos. This system combines the improved AID method with a small protein binder, enabling the control of green fluorescent protein and mCherry fusion proteins. Additionally, this system can be used to degrade tag-free targets, such as Ras proteins. We also developed caged 5-adamantyl-indole-3-acetic acid that precisely controlled targeted protein degradation under light irradiation. This advanced technique aids in the degradation of endogenous proteins of interest and can be used to develop new technologies for localized protein degradation.

overall_design: Transcriptome analysis in the AlissAID system

first: Yoshitaka

last: Ogawa

first: Kohei

last: Nishimura

first: Takumi

last: Kamura


title: Effects of magnolin and chloroform parts of Flos Magnoliae on gene expression in NCI-H1975 cells,and genetic changes after EGFR TKI resistance

status: Public on Sep 16 2025

first: wu

last: qing

state: shanxi

address: zhangjiacun

institute: Xi'an Jiaotong University

summary: we demonstrated that N-Myc Downstream Regulated 1 (NDRG1) interacts with and restrains Neuregulin 2 (NRG2) to down-regulate the EGFR. This inhibition prevents excessive autophagy protection, thereby reducing EGFR TKI drug resistance in lung cancer cell lines and xenograft mouse models. Activation of NDRG1 using compounds like Chinese herb extract Flos Magnoliae and its active monomer (magnolin) restored sensitivity in resistant cell lines to EGFR TKIs and delayed resistance in lung cancer xenograft mice. These findings highlight a mechanism for resistance to a molecularly targeted therapy and provide a potential therapeutic target for overcoming resistance to EGFR TKIs, including the second-generation inhibitor afatinib

overall_design: To investigate the genetic changes after EGFR TKI resistance and to find the inhibitors of resistance genes

first: Qing

last: Wu


title: Heat shock induces silent ribosomes and reorganizes mRNA turnover

status: Public on Sep 10 2025

city: Basel

first: Attila

last: Becskei

state: Basel-Stadt

address: Spitalstrasse 41

department: Biozentrum

summary: mRNAs associate with single or multiple ribosomes; these ribosomal assemblies —monosomes and polysomes — translate the mRNAs before degradation. The impact of heat stress on this mRNA turnover remains unclear. In heat-shocked yeast cells, the proportion of monosomes within the ribosomal assemblies rises without a corresponding increase in the number of mRNAs associated with them. As a result, most monosomes are devoid of mRNAs and silent, lacking translational initiation factors and proteins facilitating posttranslational folding. The accumulation of silent ribosomes generally reduces the rate of association of transcripts with the ribosomes. However, elevated temperatures enhance the ribosomal association of specific mRNAs, primarily those encoding heat-shock proteins, allowing them to balance their increased degradation rates. Additionally, reduced binding of the Xrn1 exonuclease to mRNAs diminishes the influence of codon optimality on mRNA stability. These mechanisms reconfigure the translation machinery to prioritize heat-shock protein synthesis over ribosome biogenesis.

overall_design: We carried out polysome profiling of yeast BY4743 strains, at standard conditions and heat shock (30°C and 42°C), and carried out RNASeq without rRNA depletion of each of the pools with them corresponding to specific ribosomal complexations of mRNA.

first: Sayanur

last: Rahaman

first: Nicole

last: Schiffelholz

first: Nitish

last: Mittal

first: Klemens

middle: E

last: Fröhlich

first: Mihaela

last: Zavolan


title: Gene expression profile at single cell level of thymic stromal cells

status: Public on Sep 09 2025

city: Vienna

first: Sergey

last: Isaev

address: Spitalgasse, 4

department: Department of Neuroimmunology

country: Austria

institute: Medical University of Vienna

summary: Thymic atrophy and the progressive immune decline that accompanies it is a major health problem, chronically with age and acutely with immune injury. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of mesenchymal niche cells (ThyMC) in human and murine thymi.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Human (n=3) and murine (n=15) thymi were disaggregated, CD45- enriched and profiled using the Chromium Single Cell 3’ Library and Gel Bead Kit v2 and v3 (10X Genomics).

first: Karin

last: Gustafsson


title: Plat safeguards aged mouse oocytes against programmed cell death through activating the Erk1/2 pathway

status: Public on Sep 13 2025

city: Nanjing

first: Xi

last: Wang

address: Longmian Avenue 101, Jiangning District

institute: Nanjing Medical University

summary: Female reproductive aging is characterized by the decline in oocytes quality and developmental potentials, but the underlying mechanisms remain insufficiently investigated. In this study, we analyze the transcriptomes of individual oocytes from young and aged mice, identifying a distinct group of aged oocytes, which display morphological abnormalities, such as fragmentation and darkened cytoplasm. These defective aged oocytes show a global shrink in gene expression, with yet a notable expression increase in mitochondrial RNA. Further gene expression analysis indicates that these defective oocytes exhibit typical features of programmed cell death (PCD), and functional assays demonstrate that those oocytes are specifically subject to both apoptosis and ferroptosis. Blocking the PCD pathways largely reverses the defective morphology. Interestingly, the expression of tissue-type plasminogen activator (tPA, or Plat) decreases with age, and even becomes undetectable in defective oocytes. Loss of Plat expression in oocytes downregulates Erk1/2 pathway activity, closely resembling the effects observed in Erk1/2 deficiency. Combining with tPA-interactome assay, it is suggested that Plat functions as an upstream regulator of Erk1/2 pathway activity, likely through Erk1/2 phosphorylation. Supplementing exogenous tPA in oocyte cultures reduces defect rate and therefore improves oocyte quality. Collectively, our findings highlight Plat as a pivotal factor in protecting aged mouse oocytes from PCD, with potential implications for developing better clinical strategies to enhance oocyte quality in aging females.

overall_design: Oocytes from young and aged mice were collected for transcriptome sequencing and comparison. Regarding the role of Plat in programmed cell death of aged oocytes, we also compared the transcriptomes of Plat-deficient oocytes versus controls.

first: Yuanlin

last: He

first: Xingsi


title: MEK5/ERK5 inhibition sensitizes NRAS-mutant melanoma to MAPK-targeted therapy by preventing Cyclin D/CDK4-mediated G1/S progression

status: Public on Sep 01 2025

city: Wuerzburg

first: Rupesh

last: Paudel

state: Bavaria

address: Josef-Schneider Straße 2

department: Department of Dermatology, Venerology und Allergology

institute: University Hospital Wuerzburg

summary: Despite the advent of immune-oncological therapies, patients with advanced NRAS-mutant melanoma still have a significantly worse prognosis than their BRAF-mutant counterparts. This is mainly due to a high propensity for resistance to available therapies targeting the RAS/RAF/MEK/ERK mitogen-activated protein kinase (MAPK) pathway (MAPKi). Preclinical studies and mouse models have implicated the stress-activated MEK5/ERK5 MAPK cascade as a major resistance pathway activated by MAPKi-based targeted therapy in NRAS-mutant melanoma. Accordingly, MAPKi/ERK5i co-inhibition was capable of triggering a sustained cell cycle arrest in NRAS-mutant melanoma cells, but the key mediator(s) of its vigorous anti-proliferative effect remain elusive. Here, we further investigated the mechanism of MAPKi/ERK5i-induced cell cycle arrest in NRAS-mutant melanoma cells using both genetic methods and pharmacological inhibitors. Transcriptome analysis of human NRAS-mutant melanoma cells established that MAPKi/ERK5i-induced a near-complete shutdown of the mitotic machinery as consequence of a sustained G1 cell cycle arrest. This arrest was not only observed in diverse treatment-naïve melanoma cells but could also be induced in cells that already had developed resistance to therapeutic MEK inhibition (MEKi) and was accompanied by suppression of Cyclin D1 and E2F-mediated gene expression. Forced expression of Cyclin D1 and its effector kinase CDK4 restored cell cycle progression and mitotic gene expression in NRAS-mutant melanoma cells exposed to MEKi/ERK5i, implying Cyclin D/CDK4 activity as major target of combined MEKi/ERK5i. These findings suggest Cyclin D/CDK4 dependency as a major vulnerability of NRAS-mutant melanoma that could effectively be targeted by combined MAPKi/ERK5i.

overall_design: NRAS-mutant melanoma cell line FM79 were seeded in triplicate and transfected with either scrambled siRNA or siRNA against MEK5. The following day, siRNA-transfected cells were either mock-treated or treated with 5 nM Trametinib for 48 hours prior to lysis and RNA extraction. Total RNA was used to perform RNA-seq experiment.

first: Simon

last: Goller

first: Felix

last: Deutzmann

first: Alina

last: Gillitzer

first: Katharina

last: Meder

first: Andrea

last: Knorz

first: David

last: Schrama

first: Matthias

last: Goebeler

first: Marc

last: Schmidt


title: Transcriptional regulator SATB1 limits CD8 T cell population expansion and effector differentiation in chronic infection and cancer [ATAC-Seq]

first: Lachlan

last: Dryburgh

summary: Chromatin accessibility profiling of SATB1 deficient and control exhausted CD8+ T cell populations in chronic infection


title: White and Brown Adipose Tissue Share a Convergent Fibro-Adipogenic Progenitor Population

status: Public on Aug 31 2025

city: Madison

last: Galmozzi

state: WI

address: 6151 WIMR, 1111 Highland Av, WIMR I, room 6151

institute: UW Madison SMPH

summary: Adipose tissue heterogeneity has emerged as a central factor in regulating adipose tissue function in physiology and pathophysiology, yet tools to model and study this diversity in vitro remain limited. Here, we performed single-cell RNA sequencing on cultured primary white and brown preadipocytes to assess how in vitro conditions impact progenitor identity. We identified two major subpopulations in both depots: committed adipogenic precursors (CAPs) and fibro-adipogenic progenitor-like cells (FAPLs). Remarkably, FAPLs were also present in brown adipose tissue, expanding the known landscape of progenitor populations in this depot. Trajectory and regulon analyses revealed that both white and brown FAPLs exhibit similar pro-fibrotic, stress-responsive signatures and diverge early from proliferating progenitor states. Integration of datasets showed that FAPLs from both depots cluster together, emphasizing their conserved identity, while CAPs remain depot-specific. Comparison to previously published in vivo single-cell datasets revealed that these in vitro populations, including brown adipose FAPLs, correspond to adipose-resident progenitor subtypes, validating the physiological relevance of this model for studying adipose tissue heterogeneity and development.

overall_design: SVF fraction of white (WAT) and brown (BAT) adipose depot from male and female C57/BL6J neonates (P0) were harvested and cultured until confluency. ScRNA-seq were performed on these cells using the 10X Genomics platform.

first: Hoang

middle: V

last: Bui

first: Julia

middle: K

last: Hansen


title: Effect of C3orf58 or SLC39A9 knock-out on gene expression in human RPE-1 cells

city: Montreal

first: Rhalena

middle: Amber

last: Thomas

state: QC

address: 3801 rue University, Montreal Neurological Institute, NW B150

department: Neurology

institute: McGill University

summary: Synucleinopathies are characterized by the accumulation and propagation of α-synuclein (α-syn) aggregates throughout the brain, leading to neuronal dysfunction and death. In this study, we used an unbiased FACS-based genome-wide CRISPR/Cas9 knockout screening to identify genes that regulate the entry and accumulation of α-syn preformed fibrils (PFFs) in cells. We identified key genes and pathways specifically implicated in α-syn PFFs intracellular accumulation, including heparan sulfate proteoglycans (HSPG) biosynthesis and Golgi trafficking. All confirmed hits affected heparan sulfate (HS), a post-translational modification known to act as a receptor for proteinaceous aggregates including α-syn and tau. Intriguingly, deletion of SLC39A9 and C3orf58 genes, encoding respectively a Golgi-localized exporter of Zn2+, and the Golgi-localized putative kinase DIPK2A, specifically impaired the uptake of α-syn PFFs, by preventing the binding of PFFs to the cell surface. Mass spectrometry-based analysis of HS chains in SLC39A9 -/- and C3orf58 -/- cells indicated major defects in HS maturation. Additionally, Golgi accumulation of NDST1, a prime HSPG biosynthetic enzyme, was detected in C3orf58 -/- cells. Interestingly, C3orf58 -/- human iPSC-derived microglia and dopaminergic neurons exhibited a strong reduction in their ability to internalize α-syn PFFs. Altogether, our data identifies new modulators of HSPGs that regulate α-syn PFFs cell surface binding and uptake.

overall_design: Total RNA sequencing of wild type RPE-1 cells and monoclonal knock-out lines for each gene SLC39A9 or C3orf58. Triplicate sample were analyzed for each genotype (WT, C3orf58 -/-, SLC39A9 -/-). RNA transcripts were calculated and differential gene expression was analyzed to access the effect of each gene on transcription.

first: Benoit

last: Vanderperre

middle: A


title: SKP1A-mediated degradation of PRC2 triggers activation of Polycomb-silenced gene [ChIP-seq]

city: Yokohama

first: Shinsuke

last: Ito

state: Kanagawa

address: 1-7-22 Suehirocho

department: IMS

institute: RIKEN

summary: Polycomb group (PcG) proteins are evolutionarily conserved repressors of developmental genes. Paradoxically, the same PcG proteins also play roles in gene activation via mechanisms that are not yet fully understood. Here, we found that S-phase kinase-associated protein 1A (SKP1A), an essential factor of SCF (SKP1A/CULLIN1/F-box) ubiquitin ligases and a subunit of the PCGF1 (Polycomb group RING finger protein 1) component of Polycomb repressive complex 1 (PCGF1-PRC1), mediates the link between PcG-dependent gene regulation and ubiquitin-dependent proteasomal degradation. By using differentiating mouse embryonic stem cells, we found that SKP1A removes EED, a core component of Polycomb repressive complex 2 (PRC2) that is bound to PcG target gene promoters, via proteasomal degradation, and it thereby sensitises these genes for subsequent activation. Furthermore, we show that SKP1A removes EED from the Meis2 promoter in the midbrain of developing mouse embryos, leading to Meis2 gene expression. In summary, we reveal here a previously unknown role of SKP1A in activating PcG-target genes via the proteasomal degradation of PRC2. This implies that SKP1A-containing PCGF1-PRC1 may confer reversibility on PcG-mediated gene silencing for robust spatiotemporal regulation of target genes.

overall_design: ChIP-seq analysis to investigate the localization of EED using EED WT and KO of embryonic stem cell or embryoid body.

first: Takashi

last: Kondo

first: Takaho

last: Endo

first: Junichiro

last: Takano

first: Haruhiko

last: Koseki


title: Assessing T-Cell Profile Shifts via IL-23 Inhibition by Guselkumab on Psoriasis.

city: Nagoya

first: Yoshifumi

last: Kanayama

address: 1 kawasumi, Mizuho-cho, Mizuho-ku

institute: Nagoya City University Graduate school of Medical Sciences

summary: Anti-IL-23 antibody therapies result in improvements to the underlying immunopathology of psoriasis. However, the dynamics of the immune profile after the administration of anti-IL-23 biologics, along with their association with treatment response, remain unclear investigation. We focused on guselkumab, an anti-IL-23p19 antibody, and performed a comprehensive analysis of immune cells, serum inflammatory molecules, and transcriptomics of CD4+ T cells, aiming to identify disease-modifying drug effects in psoriasis. A total of 24 biologic-naive patients were enrolled. Peripheral and skin lesional blood samples were collected at baseline and after treatment with guselkumab. We conducted FACS analysis of regulatory T cells (Tregs), resident memory T cells (TRMs), and dendritic cells, measured serum cytokine and chemokine levels, and examined gene expression changes using RNA-seq data for peripheral CD4+ T cells.

overall_design: RNA-seq of 1.0×10⁵ CD4 cells from peripheral blood before and at 4 and 12 weeks after Guselkumab administration.

first: Oki

last: Watanabe

first: Mai

last: Sakurai

first: Yuki

last: Enomoto

first: Aya

last: Yamamoto

first: Shunya

last: Mashiko

first: Yukako

last: Sugiura

first: Masahiko

last: Miyashiro

first: Junya

last: Masuda

first: Akimichi

last: Morita


title: Highly variable genomic methylation in the Beckwith-Wiedemann syndrome associated with Multi-Locus Imprinting Disturbances

status: Public on Sep 30 2025

city: Caserta

first: Francesco

last: Cecere

state: Caserta

address: Via A. Vivaldi, n. 43

department: DiStABiF

institute: University of Campania "Luigi Vanvitelli"

type: Methylation profiling by genome tiling array

summary: The expression of imprinted genes, which depends on their gamete of origin, is regulated by DNA sequences characterized by differential methylation between the maternal and paternal alleles (also known as germline differentially methylated regions or gDMRs). A common molecular defect associated with Beckwith-Wiedemann syndrome (BWS), a condition linked to overgrowth and tumors, is the loss of methylation of the KCNQ1OT1-TSS gDMR located on chromosome 11p15.5 (also known as IC2 LoM). Approximately one-third of BWS patients with IC2 LoM exhibit multi-locus imprinting disturbances (MLID). While maternal-effect variants in proteins of the oocyte subcortical maternal complex (SCMC) have been linked to MLID, the underlying mechanisms and health impacts of this epigenetic disturbance remain unclear.

overall_design:
We used the Infinium EPIC methylation array to investigate whole-genome CpG methylation in 64 BWS patients with IC2 LoM and 37 control subjects. We distinguished two patient groups, one with a variable methylation level of 24 gDMRs and the other with only IC2 LoM. We observed that the mothers of the former patient group carried more variants in maternal-effect genes than those of the latter group, and 50% of them, but none of the latter group had variants in the SCMC genes. Additionally, in the former group, the mothers were older at the time of pregnancy, and the patients showed higher variation in methylation levels of thousands of CpGs located in non-imprinted loci, including protochaderins and cancer-associated genes. We found no differences in clinical features or in the incidence of assisted reproductive technology between the two patient groups. However, multiple affected siblings and recurrent miscarriages were observed only among cases with biallelic maternal-effect SCMC gene variants. We used previous published data also from the following GSE: GSE133774 (GSM3927205, GSM3927206, GSM3927207, GSM3927208, GSM3927209, GSM3927210, GSM3927211, GSM3927213), GSE153211 (GSM4635809, GSM4635810, GSM4635811, GSM4635812, GSM4635813, GSM4635814, GSM4635794, GSM4635795, GSM4635797, GSM4635800), GSE195873 (GSM5855506, GSM5855507, GSM5855508, GSM5855509, GSM5855501, GSM5855500, GSM5855502, GSM5855510, GSM5855511, GSM5855512, GSM5855513, GSM5855514, GSM5855515, GSM5855516, GSM5855517, GSM5855503, GSM5855505, GSM5855504) and GSE224222 (GSM7017764).

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

first: Laura

last: Pignata

first: Emilia

last: D’Angelo

first: Carlo

last: Giaccari

first: Abu

last: Saadat

first: Angela

last: Sparago

first: Claudia

last: Angelini

first: Bruno

last: Hay Mele

first: Alessandro

last: Mussa

first: Giovanni

last: Battista Ferrero

first: Gioacchino

last: Scarano

first: Giulia

last: Gori

first: Emilio

last: Di Maria

first: Corrado

last: Romano

first: Luigi

last: Tarani

first: Carmelo

last: Piscopo

first: Iris

last: Scala

first: Jair

last: Antonio Tenorio

first: Pablo

last: Lapunzina

first: Flavia

last: Cerrato

first: Andrea

last: Riccio


title: Transcriptomic changes in retinal ganglion cell types associated with the disruption of cholinergic retinal waves

city: Berkeley

first: Matthew

last: Po

state: California

address: Stanley Hall

department: Chemical and Biomolecular Engineering

institute: UC Berkeley

summary: In the early stages of retinal development, a form of correlated activity known as retinal waves causes periodic depolarizations of immature retinal ganglion cells (RGCs). Retinal waves are crucial for refining visual maps in the brain's retinofugal targets and for the development of retinal circuits underlying feature detection, such as direction selectivity. Yet, how waves alter gene expression in immature RGCs is poorly understood, particularly at the level of the many distinct types of RGCs that underlie the retina’s ability to encode diverse visual features. We performed single-cell RNA sequencing on RGCs isolated at the end of the first postnatal week from wild-type (WT) mice and β2KO mice, which lack the β2 subunit of the nicotinic acetylcholine receptor, leading to the disruption of cholinergic retinal waves. Statistical comparisons of RGC transcriptomes between the two conditions reveal a weak impact of retinal waves on RGC diversity, indicating that retinal waves do not influence the molecular programs that instruct RGC differentiation and maturation. Although wave-dependent gene expression changes are modest in the global sense, we identified ~238 genes that are significantly altered in select subsets of RGC types. We focused on one gene, Kcnk9, which encodes the two-pore domain leak channel potassium channel TASK3. Kcnk9, which is highly enriched in αRGCs, was strongly downregulated in β2KO. We validated this result using in situ hybridization and performed whole-cell recording to demonstrate a significant decrease in the leak conductance in β2KO. Our dataset provides a useful resource for identifying potential targets of spontaneous activity-dependent regulation of neurodevelopment in the retina.

overall_design: RGCs from wild-type and β2KO mice at postnatal day 7 (P7) were isolated using CD90-conjugated magnetic beads and analyzed using scRNA-seq.

first: Rachana

last: Somaiya

first: Marla

last: Feller

first: Karthik

last: Shekhar


title: N-Myc and STAT Interactor Is A Endometriosis Suppressor Gene

city: HOUSTON

first: Sang

middle: Jun

last: Han

state: Texas

address: One Baylor Plaza

department: Molecular Cellular Biology

institute: Baylor College of Medicine

summary: Endometriosis is an estrogen-dependent inflammatory disease. A pivotal contributor to endometriosis is the estrogen receptor beta (ERβ), which drives the condition by impeding cell death through interferon (IFN) signaling. One noteworthy component of this cascade is the N-myc and STAT Interactor (NMI), an interferon alpha (IFNα) target gene whose expression is repressed in endometriotic lesions compared to normal endometrium. This repression is particularly pronounced in stromal cells, mediated by ERβ. The results of Western blot analyses, comparing IFNα-treated and untreated cells, demonstrate that IFNα treatment triggers cell death signaling, including apoptosis and necroptosis, in endometrial stromal cells. Intriguingly, NMI knockdown (KD) obstructed IFNα-induced cell death signaling in human endometrial stromal cells. Moreover, NMI KD amplified non-canonical IFNα pathways, such as β-Catenin/GSK3β and PI3K/AKT signaling, in endometrial stromal cells following IFNα treatment. RNA sequencing analyses unveiled that NMI KD augmented the expression of genes responsible for cell-cell adhesion and extracellular structural organization in IFNα-independent manners. These findings suggest that NMI KD plays an indispensable role in enhancing the adhesion and invasion of endometriotic cells during endometriosis progression. In summary, NMI functions as an endometriosis suppressor gene in endometriotic stromal cells, curbing the advancement of endometriosis. This intricate interplay of ERβ, IFNα signaling, and NMI offers novel insights into the mechanisms governing endometriosis development.

overall_design:
To investigate the role of NMI in endometriosis progression, we generated immortalized human endometriotic stromal cell lines (WT) and their NMI knockdown (KD) derivatives using shRNA (NMI KD).
We then treated the cells with vehicle (PBS with 0.1% Bovine Serum Albumin) or IFNα (invitrogen, 500ut/ml) for 24 hours.
Then, we analyzed and compared gene expression profiling of RNA-Seq data obtained from WT and NMI KD cells in the presence or absence of IFNα.

first: Yuri

last: Park


title: Transepithelial barrier dysfunction drives microbiota dysbiosis to initiate epithelial clock-driven inflammation

city: Taipei

first: Linda

last: Yu

address: 1 Jen-Ai Rd. Sec. 1

country: Taiwan

institute: National Taiwan University

type:
Expression profiling by array
Other

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

overall_design: Refer to individual Series

first: Yu-Chen

last: Pai

first: Yi-Hsuan

last: Li


title: Translocon remodeling during protein synthesis at the ER

status: Public on Aug 30 2025

city: Chicago

first: Zhe

last: Ji

state: ILLINOIS

address: 303 E Superior St, Lurie 6-107

institute: Northwestern University

summary: Protein biogenesis at the endoplasmic reticulum (ER) is coordinated by the Sec61 translocon whose dynamic subunit composition is essential for maintaining a functional proteome. How nascent secretory and membrane proteins recruit accessory factors to the translocon, and what controls the interplay between these factors during synthesis, is poorly understood. Here we use selective ribosome profiling to systematically define the cotranslational interactions of accessory factors for N-glycosylation (OST-A complex) and multipass membrane protein synthesis (GEL, PAT and BOS complexes). OST-A is actively recruited during translocation of long lumenal segments through an open Sec61 channel. This occurs independently of N-glycosylation acceptor sites, and is disfavored when Sec61 is closed. By contrast, the GEL, PAT and BOS complexes sample ribosomes docked at a closed Sec61 channel. Their recruitment is highly synchronized, and stabilized by newly inserted transmembrane domains (TMDs). Conversely, GEL, PAT and BOS binding is disfavored during translocation of long segments through open Sec61, or synthesis of long cytosolic segments. Analysis of large, topologically complex multipass proteins reveals that translocon composition can change repeatedly and reversibly during synthesis of a single polypeptide. These data establish a simple molecular logic underlying translocon remodeling during biogenesis of secretory and membrane proteins.

overall_design: Selective ribosome profiling of HEK293 cells expressing near-endogenous levels of Flag-tagged OST48, RPN2, TMCO1, CCDC47, and Nicalin. Both the total membrane ("input") and affinity-purified fractions ("IP") were collected for profiling.

first: Arunkumar

last: Sundaram

first: Qianru

first: Yu

last: Wan

first: Josephine

last: Tang

first: Robert

last: Keenan


title: Transepithelial barrier dysfunction drives microbiota dysbiosis to initiate epithelial clock-driven inflammation [gene expression]

summary: A time-series alteration in fecal microbiota was linked to the emergence of intraepithelial bacteria and a unique transcriptome profile in the mouse colon during IBD development.

overall_design: Use of gene array to explore specific transcriptome profiles in intestinal mucosa


title: Transepithelial barrier dysfunction drives microbiota dysbiosis to initiate epithelial clock-driven inflammation [metagenome]

overall_design: The gut microbiota in fecal and epithelial samples was analyzed in a time-series mode.


title: Anchored screening identifies transcription factor blueprints underlying dendritic cell diversity and subset-specific anti-tumor immunity [mouse  bulk RNA-seq]

status: Public on Aug 29 2025

city: Lund

first: Ilia

last: Kurochkin

state: Skane

address: BMC A12, Sölvegatan 17

country: Sweden

institute: Lund University

summary: Transcription factor cooperation is essential for specifying the heterogeneous dendritic cell (DC) lineages that orchestrate adaptive immunity, yet how it drives subset diversification remains poorly understood. Here, we employed a sequential anchored screen of 70 transcription factors using direct cellular reprogramming to identify regulators that specify type 2 conventional DCs (cDC2s) and plasmacytoid DCs (pDCs). We identified PU.1, IRF4, and PRDM1 as inducers of a pro-inflammatory cDC2B-like fate and SPIB, IRF8, and IKZF2 as mediators of an immature lymphoid DC program. Transcriptomic profiling linked these triads to lineage-specific signatures and demonstrated their requirement for subset identity. Mechanistically, lineage divergence was driven by chromatin co-engagement at subset-specific sites early in reprogramming. Functionally, reprogrammed DCs employed distinct immune mechanisms to elicit orthogonal anti-tumor responses in different tumor models. Collectively, our findings uncover transcriptional circuits that control DC diversification and pave the way to generate patient-tailored DC subsets for cancer immunotherapy.

overall_design: PIB, PIP and SII-transduced fibroblasts were FACS sorted for CD45 positive, reporter positive (tdTomato+ for all and YFP+ for SII) or reporter and CD45 positive at day 3 (d3), day 6  (d6) and day9 (d9) and profiled by bulk RNA sequencing. Untransduced MEFs, freshly isolated splenic cDC1s (CD11c+ MHCII+ XCR1+ CD11b-), cDC2s (CD11c+ MHCII+ CD11b+ XCR1-), and pDCs (CD11c+ Siglec-H+ B220+ BST2+) were included as controls.

first: Abigail

last: Altman

first: Luis

last: Henriques-Oliveira

first: Carlos-Filipe

last: Pereira


title: MAIT and other innate-like T cells integrate adaptive immune responses to modulate interval-dependent reactogenicity to mRNA vaccines [tempus]

city: Oxford

first: Lucy

last: Garner

address: Experimental Medicine, Level 5, John Radcliffe Hospital

department: Nuffield Department of Medicine

institute: University of Oxford

summary: Adenoviral (Ad) vectors and mRNA vaccines exhibit distinct patterns of immune responses, with reactogenicity influencing their use during and beyond the COVID-19 pandemic. However, despite the clinical significance, the underpinning mechanisms remain unclear. Innate and innate-like lymphocytes, such as mucosal-associated invariant T cells, are highly sensitive to cytokines and can enhance both innate and adaptive vaccine responses. We compared longitudinal human immune responses and reactogenicity following homologous ChAdOx1 nCoV-19 and BNT162b2 vaccination to define the interactions between innate-like lymphocytes and adaptive immunity – and their in vivo consequences. Specifically, Ad vector priming elicited robust early type I interferon (IFN)-mediated activation of innate-like T cells, augmenting T cell responses (innate to adaptive signalling), which diminished upon boosting in the presence of anti-vector immunity. In contrast, mRNA vaccine responses in innate-like cells were markedly enhanced after boosting. This was initiated by IFN-γ signalling from spike-specific memory T cells and amplified by IFN-γR+ innate-like lymphocyte networks (adaptive to innate signalling). Importantly, extending the interval between doses reduced inflammatory responses to mRNA vaccination. In an independent clinical trial, spike-specific T cells predicted severe reactogenicity to mRNA vaccine boosting regardless of the dosing interval and vaccine type. These findings reveal a close integration of innate-like and adaptive responses to novel vaccines, including an IFN-γ-mediated function of innate-like T cells in orchestrating critical early responses to mRNA vaccines which may have significant implications for optimising future vaccine regimens.

overall_design: To investigate longitudinal early immune responses to SARS-CoV-2 vaccines, we recruited 56 healthy adult volunteers and healthcare workers (HCW) prior to their initial homologous prime-boost vaccination with BNT162b2 or ChAdOx1 nCoV-19 (also known as AZD1222; hereafter referred to as ChAdOx1-S). Samples were collected at early time points following vaccination. The vaccination regimens included: BNT162b2 with a short-interval boost (n = 17; median interval, 21 days; IQR, 21-24; range, 17-30), BNT162b2 with a long-interval boost (n = 19; median interval, 70 days; IQR, 62-78; range, 42-120), and ChAdOx1-S with a long-interval boost (n = 20; median interval, 76 days; IQR, 70-79; range, 60-98). The cohort had a female bias (64%), with a median age of 35 years (IQR, 30-43; range 21-65), and a median body mass index (BMI) of 23.4 kg/m2 (IQR, 20.3-26.0). Some participants had a prior history of SARS-CoV-2 infection, evidenced by detectable anti-spike IgG antibodies at baseline. Prior infection rates were balanced among the vaccine groups, and unless otherwise stated, analyses focused on infection-naïve participants.  Peripheral blood samples were collected in EDTA, Tempus RNA, and serum separator tubes (SST) at baseline (V1), one day post-prime (V1+1), pre-boost (V2), and one day post-boost (V2+1). Adaptive immune responses were assessed four weeks post-prime (V1+28), eight weeks post-prime (V1+70) for the long-interval groups, and four weeks post-boost (V2+28), measuring SARS-CoV-2 specific binding antibodies, neutralising antibodies, and spike-specific T cell IFN-γ ELISpot responses. Due to differing dosing intervals, V1+28 corresponds to V2 for the short-interval BNT162b2 group, while V1+70 corresponds to V2 for the long-interval BNT162b2 and ChAdOx1-S groups. EDTA samples were processed to obtain plasma and peripheral blood mononuclear cells (PBMCs). Fresh PBMCs were used to phenotype cellular activation, while frozen PBMCs were used for ELISpot assays. RNA-sequencing (RNA-seq) was performed on samples collected in Tempus RNA tubes or from PBMCs, as appropriate.

first: Ali

last: Amini

first: Nicholas

middle: M

last: Provine

first: Paul

last: Klenerman


title: Cas9 senses CRISPR RNA abundance to regulate CRISPR spacer acquisition

city: Ann Arbor

first: Zhonggang

last: Hou

state: Michigan

address: 1150 W Medical Center Dr.

department: Biological Chemistry

institute: University of Michigan

summary: Prokaryotes create adaptive immune memories by acquiring foreign DNA snippets, known as spacers, into the CRISPR array1. In type II CRISPR-Cas systems, the RNA-guided effector Cas9 also assists the acquisition machinery by selecting spacers from protospacer adjacent motif (PAM)-flanked DNA2,3. Here, we uncover the first biological role for Cas9 that is independent of its dual RNA partners. Following depletion of crRNA and/or tracrRNA, Neisseria apoCas9 stimulates spacer acquisition efficiency. Physiologically, Cas9 senses low levels of crRNA in cells with short CRISPR arrays – such as those undergoing array neogenesis or natural array contractions – and dynamically upregulates acquisition to quickly expand the small immune memory banks. As the CRISPR array expands, rising crRNA abundance in turn reduces apoCas9 availability, thereby dampening acquisition to mitigate autoimmunity risks associate with elevated acquisition. While apoCas9’s nuclease lobe alone suffices for stimulating acquisition, only full-length Cas9 responses to crRNA levels to boost acquisition in cells with low immunity depth. Finally, we show that this activity is evolutionarily conserved across multiple type II-C Cas9 orthologs. Altogether, we establish an auto-replenishing feedback mechanism in which apoCas9 safeguards CRISPR immunity depth by acting as both a crRNA sensor and a regulator of spacer acquisition.

overall_design:
Examination of new CRISPR memories (i.e., spacers) formed in the N. meningitidis CRISPR-Cas9 system

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

first: Xufei

last: Zhou

first: Rucheng

last: Diao

first: Xin

first: Christine

last: Ziegler

first: Max

last: Gramelspacher

first: P. Lydia

last: Freddolino

first: Yan

last: Zhang


title: MAIT and other innate-like T cells integrate adaptive immune responses to modulate interval-dependent reactogenicity to mRNA vaccines [MAIT]

overall_design: To investigate longitudinal early immune responses to SARS-CoV-2 vaccines, we recruited 56 healthy adult volunteers and healthcare workers (HCW) prior to their initial homologous prime-boost vaccination with BNT162b2 or ChAdOx1 nCoV-19 (also known as AZD1222; hereafter referred to as ChAdOx1-S). Samples were collected at early time points following vaccination. The vaccination regimens included: BNT162b2 with a short-interval boost (n = 17; median interval, 21 days; IQR, 21-24; range, 17-30), BNT162b2 with a long-interval boost (n = 19; median interval, 70 days; IQR, 62-78; range, 42-120), and ChAdOx1-S with a long-interval boost (n = 20; median interval, 76 days; IQR, 70-79; range, 60-98). The cohort had a female bias (64%), with a median age of 35 years (IQR, 30-43; range 21-65), and a median body mass index (BMI) of 23.4 kg/m2 (IQR, 20.3-26.0). Some participants had a prior history of SARS-CoV-2 infection, evidenced by detectable anti-spike IgG antibodies at baseline. Prior infection rates were balanced among the vaccine groups, and unless otherwise stated, analyses focused on infection-naïve participants.  Peripheral blood samples were collected in EDTA, Tempus RNA, and serum separator tubes (SST) at baseline (V1), one day post-prime (V1+1), pre-boost (V2), and one day post-boost (V2+1). Adaptive immune responses were assessed four weeks post-prime (V1+28), eight weeks post-prime (V1+70) for the long-interval groups, and four weeks post-boost (V2+28), measuring SARS-CoV-2 specific binding antibodies, neutralising antibodies, and spike-specific T cell IFN-γ ELISpot responses. Due to differing dosing intervals, V1+28 corresponds to V2 for the short-interval BNT162b2 group, while V1+70 corresponds to V2 for the long-interval BNT162b2 and ChAdOx1-S groups. EDTA samples were processed to obtain plasma and peripheral blood mononuclear cells (PBMCs). Fresh PBMCs were used to phenotype cellular activation, while frozen PBMCs were used for ELISpot assays. RNA-sequencing (RNA-seq) was performed on samples collected in Tempus RNA tubes or from PBMCs, as appropriate.  Sorting of human mucosal-associated invariant T (MAIT) cells: Thawed PBMCs (2 × 106/sample) were stained with MR1 tetramers (40 min, room temperature), washed twice, then incubated with surface antibodies in FACS buffer (20 min, 4°C). Dead cells were stained using SYTOX Green (Thermo Fisher Scientific; 1:6000 dilution). Viable MAIT cells (CD3+MR1/5-OP-RU+Vα7.2-TCR+) resuspended in PBS + 0.05% BSA were sorted on a BD FACSAria III (BD Biosciences) using an 85 μm nozzle directly into 1 ml of TRIzol (Ambion, #15596026), immediately snap frozen on dry ice, and stored at −80°C until RNA extraction.


title: MAIT and other innate-like T cells integrate adaptive immune responses to modulate interval-dependent reactogenicity to mRNA vaccines


title: Platelets induce endothelial cell mitochondrial dysfunction in myocardial infarction

city: New York City

first: Florencia

last: Schlamp

state: New York

address: 435 East 30th Street

institute: NYU Langone Health

summary: Coronary endothelial dysfunction playsa key role in the pathogenesis of cardiovascular events. In the setting of myocardial infarction (MI), activatedplatelets release prothrombotic and proinflammatory factors, contributing to vascular injury and dysfunction.However, the effect of platelets on coronary endothelial function during MI is not fully understood. We investigated the effect of platelets from patients with MI on cultured coronary endothelial cells in vitro.

overall_design: Human coronary artery endothelial cells (HCAECs) from one donor were treated with platelet releasate from patients with myocardiol infarction or controls for 6 hours. Another group of HCAECs were treated with CCL3 (100 ng/mL) or PBS for 6 hours.

first: Haoyu

last: Sun

first: Sarah

last: Liberow

first: Nathaniel

middle: R

last: Smilowitz

first: Judith

last: Hochman

first: Harmony

last: Reynolds

first: Tessa

last: Barrett

first: Jeffrey

last: Berger


title: FACT depletion demonstrates a role for nucleosome organization in TAD formation [1]

city: Göttingen

first: Clemens

last: Mauksch

address: Am Faßberg 11

institute: Max-Planck-Institut für Multidisziplinäre Naturwissenschaften

summary: Mammalian genomes are organized into distinct chromatin structures, which include small-scale nucleosome arrays and large-scale topologically associating domains (TADs). The mechanistic interplay between chromatin structures across scales is poorly understood. Here, we investigate how changes in nucleosome architecture impact TAD organization by studying the role of the histone chaperone facilitates chromatin transcription (FACT) in 3D genome organization. We show that FACT depletion perturbs TADs, causing decreased insulation and weaker CTCF loops. These changes in TAD structure cannot be attributed to changes in chromatin occupancy of CTCF or cohesin and occur specifically in transcribed regions of the genome where we observe perturbed nucleosome organization in absence of FACT. FACT depletion therefore allows us to separate the role of CTCF binding from nucleosome architecture and to demonstrate that the organization of nucleosomes at TAD boundaries directly contributes to TAD formation.

overall_design: Micro-C experiments. Studies of Chromatin Conformation capture in SSRP1 depleted and non-depleted cells.

first: Yi

last: Zhu

first: Taras

last: Velychko

first: Spyridoula

last: Sagropoulou

first: Abrar

last: Aljahani

first: Shyam

last: Ramasamy

first: Kristina

last: Žumer

first: Marieke

last: Oudelaar


title: Targeting RhoA nuclear mechanoactivity rejuvenates aged hematopoietic stem cells [scRNA-seq]

city: Hospitalet de Llobregat

first: Maria Carolina

last: Florian

state: Barcelona

address: Gran Via de l’Hospitalet, 199

country: Spain

institute: Bellvitge Biomedical Research Institute (IDIBELL)

summary: Biomechanical alterations contribute to the decreased regenerative capacity of hematopoietic stem cells (HSCs) upon aging. RhoA is a key regulator of mechanosignaling, but its role in mechanotransduction in stem cell aging remains unclear. Here we show that murine HSCs respond to increased nuclear envelope (NE) tension by inducing NE translocation of P-cPLA2, which cell-intrinsically activates RhoA. Aged HSCs experience physiologically higher intrinsic NE tension, but reducing RhoA activity lowers NE tension in aged HSCs. Feature image analysis of HSC nuclei reveals that chromatin remodeling is associated with RhoA inhibition, including restoration of youthful levels of the heterochromatin marker H3K9me2 and a decrease in chromatin accessibility and transcription at retrotransposons. Finally, we demonstrate that RhoA inhibition upregulates Klf4 expression and transcriptional activity, improving aged HSC regenerative capacity and lympho/myeloid skewing in vivo. Together, our data outline an intrinsic RhoA-dependent mechanosignaling axis, which can be pharmacologically targeted to restore aged stem cell function.

overall_design: Comparative gene expression profiling analysis of scRNA-seq data from young, aged and aged treated with RhoA-inhibitor (Ri) LSKs. For each condition, 3 biological replicates were performed. LSKs were sorted from bone marrow cells as Lin- Sca1+ cKit+.

first: Eva

last: Mejía-Ramírez

first: Sara

last: Montserrat-Vazquez

first: Maria

middle: C


title: Meta-analysis of the brain transcriptomes of multiple genetic mouse models of schizophrenia highlights dysregulation in striatum and thalamus

city: Cambridge

first: Morgan

last: Sheng

state: MA

address: 75 Ames St

institute: Broad Institute of MIT and Harvard

summary: Schizophrenia is a severe mental illness with high heritability, but its underlying mechanisms are poorly understood. We meta-analyzed large-scale brain transcriptomic data from mice harboring individual loss-of-function mutations in seven schizophrenia risk genes (Akap11, Dagla, Gria3, Grin2a, Sp4, Srrm2, Zmym2). While all studied brain regions were affected, the striatum and the thalamus emerged as key brain regions of convergence. Striatum showed downregulation of synapse- and oxidative phosphorylation-related gene sets in all models. In the thalamus, mutants separated into two groups based on transcriptomic phenotype: synapse-related gene sets were upregulated in mutants with only schizophrenia and bipolar association, and were downregulated in mutants that are associated with developmental delay/intellectual disability in addition to schizophrenia. Overall, our meta-analysis reveals convergence and divergence in brain transcriptomic phenotype in these schizophrenia genetic models, supports the involvement of striatal disturbance and synapse dysfunction in schizophrenia, and points to a key role of the thalamus.

overall_design: We performed bulk RNA sequencing in 6 brain regions (hippocampus, prefrontal cortex, somatosensory cortex, substantia nigra, striatum, thalamus) and 2 ages (4-week, 12-week) in Dagla mutant mice and wild type littermates. We also performed bulk RNA sequencing of substantia nigra at 2 ages (4-week, 12-week) in Grin2a and Grin2b mutant mice and their wild-type littermates.

first: Kira

last: Perzel Mandell

first: Zohreh

last: Farsi


title: Anchored screening identifies transcription factor blueprints underlying dendritic cell diversity and subset-specific anti-tumor immunity [mouse scRNA-seq]

first: Ilia

last: Kurochkin

overall_design: Single cell RNAseq profiling on single cells, generated after transduction of mouse embryonic fibroblasts (MEFs) with Pu.1, Irf8; Pu.1, Irf8, Baft3; Pu.1, Irf4; Pu.1, Irf4, Prdm1; Spib, Irf8; Spib, Irf8, Ikzf2 at day 3 and day 9. Single cell RNAseq profiling of MEFs and CD11c+MHC-II+CD8α+ cDC1s, CD11c+MHC-II+CD11b+ cDC2s and CD11c+SiglecH+B220+BST2+ pDCs isolated from spleen were used as controls.

first: Luís

last: Henriques-Oliveira

first: Abigail

last: Altman

first: Carlos-Filipe

last: Pereira


title: Targeting RhoA nuclear mechanoactivity rejuvenates aged hematopoietic stem cells [bulk ATAC-seq confinement]

overall_design: Comparative chromatin accessibility profiling analysis of bulk ATAC-seq data from young LT-HSCs confined under a height of 5um and young control LT-HSCs. For each condition, 3 biological replicates were performed. LT-HSCs were sorted from bone marrow cells as Lin- Sca1+ cKit+ CD34- Flt3-.


title: Combination LIGHT overexpression and checkpoint blockade disrupts the tumor immune environment eradicating colorectal liver metastases

city: San Francisco

first: Bridget

middle: P

last: Keenan

state: CA

address: 505 PARNASSUS AVE, ROOM 1296

institute: University of California San Francisco

summary: Liver metastases contribute to resistance to cancer immunotherapy across tumor types and thus disrupting the immunosuppressive microenvironment of liver metastases is a therapeutic challenge. The expression of LIGHT, an immunostimulatory cytokine, can increase tumor-infiltrating T cells into colorectal cancer liver metastases and form tertiary lymphoid structures. We investigated the effect of combined anti-CTLA-4 and LIGHT expression in a mouse model of liver metastasis, demonstrating synergistic effects on tumor control, Treg-mediated suppression, and T cell activation, proliferation, and exhaustion. While intratumoral LIGHT or anti-CTLA-4 alone induced tumor-associated macrophages (TAM), only the combination led to a decrease in TAM and MDSC populations and activation of dendritic cells. The combination of LIGHT and anti-CTLA-4 represents a strategy of overcoming immunosuppression in colorectal cancer as well as other microsatellite stable tumors in which liver metastases drive resistance to immunotherapy.

overall_design: CT26 tumors (control) or CT26/LIGHT-expressing tumors were injected into BALB/c mice via splenic injection. Mice were dosed with intraperitoneal anti-CTLA-4 or isotype control on days 4, 7, 10 and 13 after tumor cell inoculation. CD45+ immune cells from the liver metastases were isolated by Fluorescence-activated cell sorting (FACS) and analyzed using scRNAseq with the 10x Genomics platform.

first: Guilin

last: Qiao

first: Nicholas

last: Kunda

first: Lyonell

last: Kone

first: Sophia

last: Guldberg

first: Prabhakaran

last: Kumar

first: Tommaso

last: Pollini

first: Jianzhong

last: Qin

first: Lawrence

last: Fong

first: Matthew

middle: H

last: Spitzer

first: Bellur

last: Prabhakar

first: Ajay

last: Maker


title: FACT depletion demonstrates a role for nucleosome organization in TAD formation [2]

first: Clemens

last: Mauksch

first: Yi

last: Zhu

first: Taras

last: Velychko

first: Spyridoula

last: Sagropoulou

first: Abrar

last: Aljahani

first: Shyam

last: Ramasamy

first: Kristina

last: Žumer

first: Marieke

last: Oudelaar


title: Regulation of the NSL complex by TAF4A is critical for genome stability and quiescence of skeletal muscle stem cells.

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

institute: Max Planck Institute for Heart and Lung Research


title: Anchored screening identifies transcription factor blueprints underlying dendritic cell diversity and subset-specific anti-tumor immunity [human ChIP-seq]

first: Ilia

last: Kurochkin

overall_design: Examination of global occupancy for PU.1, IRF4, PRDM1 and SPIB, IRF8, IKZF2 together or individually at day 2 of cDC2 and pDC reprogramming in HDFs.

first: Luís

last: Henriques-Oliveira

first: Abigail

last: Altman

first: Carlos-Filipe

last: Pereira


title: FACT depletion demonstrates a role for nucleosome organization in TAD formation


title: Targeting RhoA nuclear mechanoactivity rejuvenates aged hematopoietic stem cells [bulk ATAC-seq]

first: Maria Carolina

last: Florian

overall_design: Comparative chromatin accessibility profiling analysis of bulk ATAC-seq data from young, aged and aged treated with RhoA-inhibitor (Ri) LT-HSCs. For each condition, 4-5 biological replicates were performed. LT-HSCs were sorted from bone marrow cells as Lin- Sca1+ cKit+ CD34- Flt3-.

first: Eva

last: Mejía-Ramírez

first: Sara

last: Montserrat-Vazquez

first: Maria


title: Targeting RhoA nuclear mechanoactivity rejuvenates aged hematopoietic stem cells

overall_design: Refer to individual Series