title: Spatial genomics reveals cholesterol metabolism as a key factor in immunotherapy resistance in colorectal cancer [Visium]

status: Public on Mar 10 2025

city: Cambridge

first: Andrew

middle: J

last: Kavran

state: MA

address: 250 Water Street

institute: Bristol Myers Squibb

summary: Immune checkpoint inhibitors (ICIs) have transformed the treatment landscape across multiple cancer types achieving durable responses for a significant number of patients. Despite their success, many patients still fail to respond to ICIs or develop resistance soon after treatment. We sought to identify early treatment features associated with ICI outcome. We leveraged the MC38 syngeneic tumor model because it has variable response to ICI therapy driven by tumor intrinsic heterogeneity. ICI response was assessed based on the level of immune cell infiltration into the tumor – a well-established clinical hallmark of ICI response. We generated a spatial atlas of 48,636 transcriptome-wide spots across 16 tumors using spatial transcriptomics; given the tumors were difficult to profile, we developed an enhanced transcriptome capture protocol yielding high quality spatial data. In total, we identified 8 tumor cell subsets (e.g., proliferative, inflamed, and vascularized) and 4 stroma subsets (e.g., immune and fibroblast). Each tumor had orthogonal histology and bulk-RNA sequencing data, which served to validate and benchmark observations from the spatial data. Our spatial atlas revealed that increased tumor cell cholesterol regulation, synthesis, and transport were associated with a lack of ICI response. Conversely, inflammation and T cell infiltration were associated with response. We further leveraged spatially aware gene expression analysis, to demonstrate that high cholesterol synthesis by tumor was associated with cytotoxic CD8 T cell exclusion. Finally, we demonstrate that bulk RNA-sequencing was able to detect immune correlates of response but lacked the sensitivity to detect cholesterol synthesis as a feature of resistance.

overall_design: Visium spatial transcriptomics of 16 MC38 tumors harvested after 5 days of treatment with either IgG or aPD-1 antibodies.

first: Yulong

last: Bai

first: Brian

last: Rabe

last: Kreshock

last: Fisher

first: Yelena

last: Cheng

first: Anne

last: Lewin

first: Chao

last: Dai

first: Matthew

last: Meyer

first: Konstantinos

last: Mavrakis

last: Lyubetskaya

first: Eugene

last: Drokhlyansky


title: Multiple subpopulations in medullary thymic epithelial cells are regulated by Aire with distinctive modes of gene regulations [deep single-cell RNA-seq]

status: Public on Mar 12 2025

city: Tsurumi-ku, Yokohama

first: Hideyuki

last: Yoshida

state: Kanagawa

address: 1-7-22 Suehiro-cho

country: Japan

institute: RIKEN IMS

type: Expression profiling by high throughput sequencing

summary: Aire, a transcriptional regulator whose defect results in the development of autoimmunity, controls the transcriptome in the bulk of medullary thymic epithelial cells (mTECs) including the genes for self-antigens. Mechanisms for this process, however, remained incompletely understood, especially regarding the effects of Aire in each subpopulation in mTECs. Here, we combined single-cell multi-omics (scMulti-seq) technologies by which gene expression and open chromatin were simultaneously profiled from the same cell and deeper single-cell sequencing by RamDA-seq which enabled profiling of the minimum dropout. scMulti-seq effectively demonstrated the subpopulations among mTECs associated with diverse transcription factor activities which are affected by Aire and developmental stages, while RamDA-seq revealed the different modes of gene regulations by Aire in different subpopulations. Aire is not only essential for the development of a specific population in which Aire induces a set of genes in a stochastic manner but also promotes the development of multiple subpopulations in which Aire enhances the expressions of genes in a coordinated manner. The former group of Aire-induced genes was characterized by enhanced H3K27me3 chromatin modifications and Aire seems to unleash these silenced genes by deactivating polycomb repressive complex 2 (PRC2). We also found unique gene signatures for the neonatal stage such as high expression of chemokines and expression of cortical TEC (cTEC)-like genes in TECs, which were Aire-independent. Our approach has illuminated the multilayered transcriptional control in mTECs governing the multiple subpopulations organizing the thymic microenvironment.

overall_design: deep single-cell RNA-seq analysis of FACS-sorted mouse thymic epithelial cells (TECs, CD45-EpCAM+Ly51-) from wild-type and Aire knockout (KO) mice

first: Matsumoto

last: Minoru

first: Yoshida

last: Masaki

first: Miyazawa

last: Ryuichiro

first: Morimoto

last: Junko

first: Oya

last: Takeshi

first: Tsuneyama

last: Koichi

last: Mitsuru

last: Hideyuki


title: Involvement of lncRNA MIR205HG in idiopathic pulmonary fibrosis and regulation of IL33 via Alu elements

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

summary: Idiopathic pulmonary fibrosis (IPF) causes remodelling of distal lung, leading to respiratory failure. Pulmonary remodelling is characterised histologically not only by fibrosis but by also appearance of basal cells, yet the involvement of basal cells to IPF pathogenesis remains unclear. Here, we focus on the long non-coding RNA MIR205HG highly expressed in basal cells by single-cell RNA sequencing, to elucidate their role in IPF. Through RNA sequencing of genetic manipulations using primary cells and IPF-derived airway organoids, we uncovered MIR205HG to regulate IL33 expression. Mechanistically, the AluJb element of MIR205HG plays a key role in IL33 expression. In addition, we successfully identified a small molecule that targets this AluJb element and decreases IL33 expression. IL33 is known to induce ILC2, and MIR205HG expression positively correlated with the number of ILC2 in IPF patients. Collectively, these findings provide insights into the contributing mechanisms of basal cells to IPF and potential therapeutic targets.

overall_design: To examine gene expression profiles in DQzG treatment (5 µM) with NHBE cells and IPF-derived airway organoids (#3), total RNA was extracted from the cells.

first: Tsuyoshi

last: Takashima

last: Okuzaki

first: Eiichi

last: Morii


title: Colonic Epithelial-derived FGF1 Protects against Inflammatory Bowel Disease via Driving Intestinal Stem Cells Differentiation toward Goblet Cells

city: 温州

first: sudan

last: zhang

address: 瓯海

country: China

institute: wenzhou medical university

summary: Inflammatory bowel disease (IBD), characterized by impaired intestinal epithelia barrier, especially goblet cell loss, lacks effective treatment strategies. FGF1, the most abundantly expressed FGF ligand in the colon, was significantly downregulated in IBD mouse models and patients. However, the role of FGF1 in the pathogenesis of IBD, particularly in goblet cell loss, remains elusive.

overall_design: The effects of intestinal epithelial cells (IECs)-specific deletion of Fgf1 and recombinant FGF1 (rFGF1) supplementation on colonic epithelial barrier, cellular composition, and disease phenotypes in IBD mice were investigated. In vitro colonic organoids were used to analyze the effect of FGF1 on the lineage commitment of intestinal stem cells (ISCs). RNA sequencing, shRNA, and Villin-CreERT2Atoh1fl/fl and Lgr5-EGFP-CreERT2Fgfr2fl/fl mice were used to explore the molecular mechanisms by which FGF1 drives ISCs differentiation toward goblet cells.


title: Spatial genomics reveals cholesterol metabolism as a key factor in immunotherapy resistance in colorectal cancer [bulk RNA-seq]

first: Andrew

last: Kavran

country: USA

overall_design: Bulk RNA-seq of 16 MC38 tumors harvested after 5 days of treatment with either IgG or aPD-1 antibodies.

first: Yulong

last: Bai

first: Brian

last: Rabe

first: Anna

last: Kreshock

last: Fisher

first: Yelena

last: Cheng

last: Lewin

last: Dai

last: Meyer

last: Mavrakis


title: Border-zone cardiomyocytes and macrophages contribute to remodeling of the extracellular matrix to promote cardiomyocyte invasion during zebrafish cardiac regeneration

status: Public on Mar 11 2025

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

summary: Despite numerous advances in our understanding of zebrafish cardiac regeneration, an aspect that remains less studied is how newly proliferated cardiomyocytes invade, and eventually replace, the collagen-containing fibrotic tissue following injury.  Here, we provide an in-depth analysis of the process of cardiomyocyte invasion and migration using live-imaging and histological approaches.  We observed a close interaction between protruding cardiomyocytes and macrophages at the wound border zone, and irf8 mutant zebrafish, which largely lack macrophages, exhibited defects in extracellular matrix (ECM) remodeling and cardiomyocyte protrusion into the injured area.  Using a resident macrophage ablation model, we show that defects in ECM remodeling at the border zone and subsequent cardiomyocyte protrusion can be partly attributed to a population of resident macrophages.  Single-cell RNA-sequencing analysis of cells at the wound border revealed a population of cardiomyocytes and macrophages with fibroblast-like gene expression signatures, including the expression of genes encoding ECM structural proteins and ECM-remodeling proteins.  The expression of mmp14b, which encodes a membrane-anchored matrix metalloproteinase, was restricted to cells in the border zone and genetic deletion of mmp14b led to a decrease in 1) collagen degradation at the border zone, 2) macrophage recruitment to the border zone, and 3) subsequent cardiomyocyte invasion.  Furthermore, cardiomyocyte-specific overexpression of mmp14b was sufficient to enhance cardiomyocyte invasion both into the injured area and along the apical surface of the wound.  Altogether, our data shed important insights into the process of cardiomyocyte invasion of the collagen-containing injured tissue during cardiac regeneration.  They further suggest that cardiomyocytes and resident macrophages contribute to ECM remodeling at the border zone to promote cardiomyocyte replenishment of the fibrotic injured tissue.

overall_design: The border zone of regenerating wild-type zebrafish hearts at 7 dpci was microdissected and subjected to scRNA-seq

first: Arica

last: Beisaw

last: Guenther


title: Inhalable liposomal delivery of osimertinib and DNA for treating primary and metastatic lung cancer

city: Jinan

first: Xianglei

last: Fu

address: Wenhuaxi Road

institute: Shandong University

summary: Lung cancer is one of the most prevalent cancers, and brain metastases significantly worsen the prognosis for patients. We developed an inhalable surfactant-based biomimetic nanoliposome system (MPDOLs) to co-deliver Osimertinib and DNA plasmids to deplete IGF2BP3 expression. To investigate how MPDOLs influence gene expression and therapeutic outcomes by targeting IGF2BP3 and co-delivering Osimertinib, we performed transcriptomic analysis of MPDOL treated Lewis lung cancer cells.

overall_design: Lewis lung cancer cells were obtained from Procell Life Science and Technology Co., Ltd. (Wuhan, China). They were maintained in Dulbecco's modified Eagle’s medium supplemented with 10% FBS and 1% PS and were cultivated in an environment with a 5% CO2 atmosphere at 37 °C. Lewis lung cancer cells were seeded overnight and treated with MPDOLs or PBS for 48 hours. Total RNA was isolated from cultured cells using the TRIzol reagent for RNA sequencing. Agilent 2100 bioanalyzer was used to control quality and NEBNext®UltraTMRNA Library Prep Kit for Illumina® (NEB, USA) was used to generate libraries.

first: Yanbin

last: Shi

first: Hang

last: Wu

first: Yankun

last: Zhang

first: Yingying

last: Liu

first: Xiaoyu

last: Wan

first: Xiangqin

last: Chen

first: Jiamin

last: Zhou

first: Shengnan

last: Qiu

first: Xiaogang

last: Zhao

first: Zhongxian

last: Tian

first: Lian

last: Li

first: Hengchang

last: Zang

first: Guimei

last: Lin


title: Multiple subpopulations in medullary thymic epithelial cells are regulated by Aire with distinctive modes of gene regulations

first: Hideyuki

last: Yoshida

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: Involvement of lncRNA MIR205HG in idiopathic pulmonary fibrosis and regulation of IL33 via Alu elements (part 4)

first: Daisuke

last: Motooka

overall_design: To compare gene expression profiles between HTll-280+ cells (AT2 cells) (Patient_#1 and Patient_#2) and NGFR+ cells (Basal cells) (Patient_#1 and Patient_#2), total RNA was extracted from the cells.

first: Tsuyoshi

last: Takashima

last: Okuzaki

first: Eiichi

last: Morii


title: AAV vectors trigger neurotoxic DNA damage responses and STING-dependent inflammation in human CNS cells.

city: Milan

first: Monah

last: Abou Alezz

address: Via Olgettina 60

country: Italy

institute: SR-TIGET


title: Involvement of lncRNA MIR205HG in idiopathic pulmonary fibrosis and regulation of IL33 via Alu elements (part 1)

overall_design: To compare gene expression profiles between alveolar organoids (#1, #2 and #3) and IPF-derived airway organoids (#1, #2 and #3), total RNA was extracted from the cells.


title: In vivo armed macrophages curb liver metastasis through tumor reactive T cell rejuvenation (TAD19)

city: Segrate

first: Ivan

last: Merelli

state: Milano

address: via F.lli Cervi 93

department: Istituto di Tecnologie Biomediche

institute: Consiglio Nazionale delle Ricerche

summary: Despite recent progress in cancer treatment, liver metastases persist as an unmet clinical need. This is partly attributable to the immunosuppressive microenvironment of liver metastases, which inhibits immune activation. To unleash anti-tumoral immune responses against liver metastases, we armed liver and tumor-associated macrophages to coordinately express tumor antigens (TAs), IFNα and IL-12. The combination of TAs with both cytokines yielded the most potent therapeutic response, resulting in the eradication of established liver metastases in several mouse models of the disease. Mechanistically, armed macrophages expanded tumor reactive CD8+ T cells, which in the presence of IFNα and IL-12 acquired features of progenitor exhausted T cells and killed cancer cells independently of CD4+ T cell help. IFNα and IL-12 produced within the liver tissue by armed macrophages rewired cell interactions within the tumor microenvironment and reprogrammed antigen presenting cells to further support T cell effector functions. Tumor reactive T cell rejuvenation and strong therapeutic activity were observed in distinct liver metastasis mouse models of colorectal cancer and melanoma, expressing either surrogate tumor antigens, naturally occurring private neoantigens or tumor-associated antigens. Altogether, our findings support the translational potential of in vivo armed liver macrophages expressing TA and immune-activating cytokines to expand and rejuvenate tumor reactive T cells for the treatment of liver metastases.

overall_design: CD45+ positive cells were isolated from mouse liver by FACS and analysed for scRNAseq. These mice were bearing AKTPF liver metastases and were treated with Lentiviral vectors containing tumor antigen (TA) and cytokines (IL-12 and IFNa).

first: Marco

last: Notaro

first: Maristella

last: Borghetti

last: Monti

first: Stefano

last: Beretta

first: Luigi

last: Naldini

first: Mario

middle: L

last: Squadrito


title: AAV vectors trigger neurotoxic DNA damage responses and STING-dependent inflammation in human CNS cells [scRNAseq_dataset1]

summary: Adeno-associated viral (AAV) vector gene therapy is gaining ground as a treatment option for genetic neurodegenerative diseases tha currently have no cure. Nonetheless, significant toxicity and severe adverse events are emerging in recent clinical trials through mechanisms that remain unclear. We have modelled here AAV-mediated neurotoxicity in the context of the human brain taking advantage of human induced pluripotent stem cell-based technologies. We have used single-cell RNA sequencing technologies to interrogate vector-induced cell-intrinsic innate immune mechanisms that could contribute to neurotoxicity in mixed 2D neuron-glial cultures transduced with AAV vectors at different time-points and harvested at two different time-points.

overall_design: hiPSC-derived neural cultures containing a mix of neurons, astrocytes and oligodendrocytes were transduced in experimental duplicates with different AAV serotypes and harvested after 2 or 4 days post-transduction for scRNAseq. Duplicates for each condition were pooled for library preparation.

first: Helena

middle: C

last: Verdera

middle: A

last: Alezz

first: Anna

last: Kajaste-Rudnitski


title: In vivo armed macrophages curb liver metastasis through tumor reactive T cell rejuvenation (TAD12)

overall_design: CD45+ positive cells were isolated from mouse liver by FACS and analysed for scRNAseq. These mice were bearing liver metastases and were treated with Lentiviral vectors containing tumor antigen (TA) and cytokines (IL-12 and IFNa).


title: In vivo armed macrophages curb liver metastasis through tumor reactive T cell rejuvenation (TAD18)

overall_design: CD45+ positive cells were isolated from mouse liver by FACs and analysed for scRNAseq. These mice were bearing MC38.OVA  liver metastases and were treated with Lentiviral vectors containing tumor antigen (TA) and cytokines (IL-12 and IFNa).


title: In vivo armed macrophages curb liver metastasis through tumor reactive T cell rejuvenation (RNA-Seq)

overall_design: To identify novel tumor antigens in the AKTPF cell line, we performed WES and RNA sequencing on tumor samples. RNA sequencing was performed also on healthy tissues (liver and small intestine) to assess whether tumor cells overexpress specific genes that might represent putative tumor associated antigens.


title: In vivo armed macrophages curb liver metastasis through tumor reactive T cell rejuvenation (MERFISH)

overall_design: Mice bearing established liver metastases were treated with TA33 or TA33.Combo. After 10 days mice were eutanized and the liver was collected to perform spatial transcriptomics.


title: NAD+ prevents chronic kidney disease by activating renal tubular metabolism - spatial transcriptomics

city: Washington

first: Bryce

last: Jones

state: DC

address: 4000 Reservoir Rd NW

department: Pharmacology and Physiology

institute: Georgetown University

summary: Chronic kidney disease (CKD) is associated with renal metabolic disturbances, including impaired fatty acid oxidation (FAO). Nicotinamide adenine dinucleotide (NAD+) is a small molecule that participates in hundreds of metabolism-related reactions. NAD+ levels are decreased in CKD, and NAD+ supplementation is protective. However, both the mechanism of how NAD+ supplementation protects from CKD, as well as the cell types involved, are poorly understood. Using a mouse model of Alport syndrome, we show that nicotinamide riboside (NR), an NAD+ precursor, stimulates renal peroxisome proliferator-activated receptor α signaling and restores FAO in the proximal tubules, thereby protecting from CKD in both sexes. Bulk RNA-sequencing shows that renal metabolic pathways are impaired in Alport mice and activated by NR in both sexes. These transcriptional changes are confirmed by orthogonal imaging techniques and biochemical assays. Single nuclei RNA-sequencing and spatial transcriptomics, both the first of their kind from Alport mice, show that NAD+ supplementation restores FAO in proximal tubule cells. Finally, we also report, for the first time, sex differences at the transcriptional level in this Alport model. In summary, the data herein identify a nephroprotective mechanism of NAD+ supplementation in CKD, and they demonstrate that this benefit localizes to the proximal tubule cells.

overall_design: Spatial transcriptomics was performed on kidneys from 25-week-old Col4a3tm1Dec male mice on the C57BL/6J background. All four combinations of experimental groups were investigated: control versus Alport and vehicle versus nicotinamide riboside (N = 1 mouse per group, 4 mice total).


title: Correction of dysregulated lipid metabolism normalizes gene expression in oligodendrocytes and prolongs lifespan in female poly-GA C9orf72 mouse model

city: Munich

first: Dieter

last: Edbauer

state: Select...

address: Feodor-Lynenstr. 17

institute: DZNE

summary: These sequences support the following paper abstract: "Clinical and genetic research links altered cholesterol metabolism with ALS development and progression, yet pinpointing specific pathomechanisms remain challenging. We investigated how cholesterol dysmetabolism interacts with protein aggregation, demyelination, and neuronal loss in ALS. Bulk RNAseq transcriptomics showed decreased cholesterol biosynthesis and increased cholesterol export in ALS mouse models (GA-Nes, GA-CFP, rNLS8) and patient samples (spinal cord), suggesting an adaptive response to cholesterol overload. Consequently, we assessed the efficacy of the cholesterol-binding drug 2-hydroxypropyl-β-cyclodextrin (CD) in a fast-progressing C9orf72 ALS mouse model with extensive poly-GA expression and myelination deficits. CD treatment normalized cholesteryl ester levels, lowered neurofilament light chain levels, and prolonged lifespan in female but not male GA-Nes mice, without impacting poly-GA aggregates. Single nucleus transcriptomics indicated that CD primarily affected oligodendrocytes, significantly restored myelin gene expression, increased density of myelinated axons, inhibited the disease-associated oligodendrocyte response, and downregulated the lipid-associated genes Plin4 and ApoD. These results suggest that reducing excess free cholesterol in the CNS could be a viable ALS treatment strategy.”

overall_design: GA-Nes mice (LaClair et al, Acta Neuropathologica 2020) and littermate controls were treated with the cholesterol sequestering drug 2-hydroxypropyl-β-cyclodextrin (CD) or vehicle control from P21 (daily subcutaneous treatment) and harvested on P40. We aim to investigate the mechanisms of lifespan extension and neurofilament reduction with CD treatment in female mice.

first: Ali

last: Rezaei

first: Zeynep

last: Gunes

first: Sabine

last: Liebscher

first: Franz

last: Bauernschmitt

first: Eduardo

last: Beltran


title: NAD+ prevents chronic kidney disease by activating renal tubular metabolism - single nuclei RNA-sequencing

overall_design: Single-nuclei RNA-sequencing with simultaneous assay for transposase-accessible chromatin was performed on kidneys from 25-week-old Col4a3tm1Dec mice on the C57BL/6J background. All eight combinations of experimental groups were investigated: male versus female, control versus Alport, and vehicle versus nicotinamide riboside (N = 1 mouse per group, 8 mice total). Nuclei from male and female mice were pooled within the same genotype/treatment combination. This SubSeries contains the snRNA-seq data. It does not contain the snATAC-seq data.


title: Endothelial Tgfß1 supports lung interstitial  macrophage differentiation and pulmonary homeostasis

city: Liège

first: Thomas

last: Marichal

address: Avenue de l'Hopital 11

department: GIGA Institute

country: Belgium

institute: University of Liege

summary: Lung interstitial macrophages (IMs) inhabit the lung parenchyma and are thought to contribute to lung immunoregulation and homeostasis. While recent progress has been made about the development, diversity and transcriptional regulation of lung IMs, the microenvironmental signals responsible for their tissue-specific identity remain unidentified. Here we found, in mice, that lung endothelial cell-derived Tgf 1 specifically triggered a core Tgf  receptor-dependent lung IM signature in bone marrow-derived monocytes and macrophages (Macs). In vivo, myeloid-specific ablation of Tgf  receptor signaling severely impaired monocyte-to-IM development, resulting in the accumulation of perivascular monocytes, decreased IM numbers and a severe loss of IM-intrinsic identity. Of note, monocyte-to-IM development was similarly impaired in the absence of endothelial-specific Tgf 1. Functionally, mice selectively lacking Tgf  receptor in IMs exhibited a severe impairment of the lung immunoregulatory environment and prematurely developed lung hyperinflation, increased compliance and decreased elastance, changes classically associated with ageing. Our work identifies a novel endothelial - IM axis involving Tgf 1-Tgf r interactions that shapes IM identity and thereby sustains lung tissue integrity, thus providing foundations for IM-targeted interventions in the context of lung ageing and other chronic inflammatory disorders.

overall_design: CD45.1/CD45.2 IMDTR mice were lethally irradiated with thorax protection and were fully reconstituted with BM cells either from CD45.2 Tgfbr2fl/fl mice or from CD45.2 Lyz2Cre Tgfbr2fl/fl mice. Four weeks later, chimeric IMDTR mice were treated with DT to specifically empty the IM niche and trigger IM niche refilling from either control or Tgfbr2-deficient monocytes. bulk RNA-seq was performed on reconstituted IMs 10 days after DT.

first: Wen

last: Peng

first: Qiang

last: Bai

first: Joan

last: Abinet


title: NAD+ prevents chronic kidney disease by activating renal tubular metabolism - bulk RNA-sequencing

overall_design: Bulk RNA-sequencing was performed on isolated kidney cortex from 25-week-old Col4a3tm1Dec mice on the C57BL/6J background. All eight combinations of experimental groups were investigated: male versus female, control versus Alport, and vehicle versus nicotinamide riboside (N = 4 mice per group, 32 mice total).


title: In vivo armed macrophages curb liver metastasis through tumor reactive T cell rejuvenation

first: Ivan

last: Merelli

platform_organism:
Mus musculus
synthetic construct


title: STAT6 mutations compensate for CREBBP mutations and hyperactivate IL4/STAT6/RRAGD/mTOR signaling in follicular lymphoma

city: Ann Arbor

first: Karan

last: Bedi

state: MI

address: 1600 Huron Pkwy

department: Biostatistics

institute: University of Michigan

summary: Activating mutations in STAT6 are common in Follicular Lymphoma (FL) and transformed FL and various other B cell lymphomas. Here, we report RNA-seq based gene expression data on normal human lymph node derived B lymphocytes (NBC; N = 6), and primary human FL WT (N = 11) or mutant (N = 4) for STAT6 before and after ex vivo stimulation with IL4. We found that STAT6 mutants result in broad based augmentation of IL4-induced gene expression. Unexpectedly, in FL with WT STAT6 we measured reduced baseline and IL4-induced gene expression levels when compared with NBC lymphocytes or FL with STAT6 mutations. We tracked the attenuated IL4/JAK/STAT6 response to co-existing CREBBP mutations and experimentally verified that intact CREBBP is required for the induction of many IL4-induced genes. One of the IL4-induced genes here identified is RRAGD, a small G-protein involved in lysosomal mTOR activation. We show that IL4 treatment induced RRAGD expression, that RRAGD is required for mTOR activation in lymphoma cells and that IL4-enhanced BCR signaling induced mTOR activation. The IL4 and BCR-induced mTOR activation was reduced by CREBBP mutants and augmented by mutant STAT6, establishing a link between STAT6 mutations and mTOR regulated pro-growth pathways in lymphoma.

overall_design: Cryopreserved single-cell suspensions from human non-malignant lymph node (LN) biopsies or lymphomatous LNs were thawed, washed and depleted of CD3+ T cells and CD14+ macrophages using Miltenyi beads and columns (Miltenyi, 130-050-101 and 130-050-201).  The B lymphocytes were cultured for 4 h in the presence or absence of 10 ng/ml of IL4.  Total RNA was purified using the Trizol reagent followed by RNAeasy column purification (Qiagen).  RNA was assessed using the Bioanalyzer (Agilent #5067-1513) and a Qubit RNA High Sensitivity assay (Thermofisher # Q32855), and 2ng of RNA input was processed for sequencing using the Takara SMART-Seq stranded kit (#634444).

first: Qiangqiang

last: Shao

first: Sami

middle: N

last: Malek


title: DNA methylation memory of acinar-ductal transition state altering Kras-downstream Pi3k and Rho GTPase signaling [WGBS]

city: Baltimore

first: Emily

last: Lo

state: MD

address: 733 N Broadway

institute: Johns Hopkins

type: Methylation profiling by high throughput sequencing

summary: A critical area of recent cancer research is the emergence of transition states between normal and cancer that exhibit increased cell plasticity which underlies tumor cell heterogeneity. Pancreatic ductal adenocarcinoma (PDAC) arises from a transition state termed acinar-to-ductal metaplasia (ADM), in which digestive enzyme-producing acinar cells acquire a transient ductal epithelium-like phenotype while maintaining their geographical acinar organization. ADM is created by overexpression of the Kruppel-like factor 4 gene (KLF4) in the absence of oncogenic driver mutations. Here, we investigate the DNA methylation landscape and corresponding transcriptional landscape of the mutation-free ADM transition state and the subsequent reversion to a normal acinar phenotype. We ask to what extent cells retain a memory of the ADM transition state via DNA methylation, examine potential regulators of altered DNA methylation during ADM, and investigate the relationship of the ADM transition state to human pancreatic cancer precursor lesions. These findings may inform the mechanisms not only of heritable epigenetic memory of transition states and inflammation, but also of how epigenetic alterations presage or even elicit genetic mutations in cancer.

overall_design: Cell types isolated via laser-capture microdissection from normal pancreata and pancreata undergoing acinar-ductal metaplasia were analyzed using whole-genome bisulfite sequencing.

middle: K

first: Patrick

last: Cahan

first: Andrew

middle: P

last: Feinberg


title: DNA methylation memory of acinar-ductal transition state altering Kras-downstream Pi3k and Rho GTPase signaling [spatial transcriptomics]

overall_design: Normal pancreata and pancreata undergoing acinar-ductal metaplasia were analyzed using spatial transcriptomics.


title: DNA methylation memory of acinar-ductal transition state altering Kras-downstream Pi3k and Rho GTPase signaling

overall_design: Refer to individual Series


title: RNA-Seq analysis of changes in gene expression upon cell treatment with double stranded RNA

city: Warsaw

first: Pawel

middle: J.

last: Sikorski

address: Zwirki i Wigury 101

department: Faculty of Biology

country: Poland

institute: University of Warsaw

summary: The aim of the study was to analyze the impact of the 5' end modifications of double-stranded RNA on the cellular immune response.

overall_design: A549 cells were transfected for 5 h with differently modified dsRNA.

first: Krzysztof

last: Goryca

first: Dorota

last: Adamska

first: Michal

last: Szelag


title: Molecular basis for human respiratory syncytial virus transcriptional regulator NS1 interactions with MED25

status: Public on Mar 09 2025

city: St. Louis

first: Jacqueline

last: Payton

state: MO

address: 660 S. Euclid Ave

department: Pathology and Immunology

institute: Washington University School of Medicine

summary: Human Respiratory Syncytial Virus (hRSV) is a prevalent pathogen posing significant risks to infants and older adults. While the roles of RSV non-structural proteins NS1 protein in modulating host immune responses remains poorly defined, its potential impact on viral pathogenicity is critical. We employed CUT&RUN of NS1, Mediator, and ATF3 in WT NS1 and mutant NS1 expressing A549 cells and bulk RNA sequencing of WT and mutant NS1-expressing A549 (GSE155151) and RSV infection in human lung air-liquid interface (ALI) cultures to elucidate the perterbations of transcriptional regulatory control induced by NS1. Coupled with our earlier work, these epigenomic and transcriptomic profiling datasets provides deeper insights into the molecular mechanisms through which RSV NS1 protein disrupts host immune functions.

overall_design: RNA-seq profiling of human tracheobronchialepithelial cells (hTEC) mock-infected or infected with hRSV A2 strain at MOI 3 for 72 hours. CUT&RUN sequencing of NS1, Mediator, and ATF3 in WT NS1 and mutant NS1 expressing A549 cells.

first: J

middle: E

first: D

middle: W

last: Leung


title: Transcriptome of rNLS8 mice and controls injected with non-targeting control ASO

status: Public on Mar 08 2025

first: Ali

last: Rezaei

address: Feodor-Lynen-Strasse 17

institute: LMU

summary: We asked how knockdown of genes associated with neurodegeneration using antisense oligonucleotides (ASO) affects disease phenotypes in an inducible TDP-43 transgenic mouse model (rNLS8, Walker et al., Acta Neuropathologica 2015) backcrossed to the C57BL/6 background. This dataset includes only the non-targeting control, which was also used as a replication cohort for transcriptional changes in rNLS8 mice (Rezaei et al., in revision at Nature Communications). We show cholesterol dysmetabolism and marker genes of disease-associated oligodendrocytes in the brain of rNLS8 mice. Data from mice receiving the targeting ASOs will be made available upon publication of the manuscript (Kocsis-Jutka et al, in preparation).

overall_design: 17-19 week old rNLS8 mice and monogenic control littermates were injected intracerebroventricularly with a non-targeting control antisense oligonucleotide (CCTATAGGACTATCCAGGAA). As in Jiang et al. (Neuron 2016), the injection consisted of 350 µg ASO in a total volume of 10 µL. All animals were maintained on a doxycycline diet (200 mg/kg, Ssniff, Germany) until two weeks after injection. The animals were then switched to standard chow without doxycycline to induce the TDP-43ΔNLS transgene. The animals were sacrificed 3 weeks later. The experiment was done in two independent cohorts (A and B). Data from mice receiving the targeting ASO will be releases once the manuscript is published (Kocsis-Jutka et al, in preparation).

first: Virág

last: Kocsis-Jutka

first: Dieter

last: Edbauer


title: Selective identification of epigenetic regulators at methylated genomic sites by SelectID [ChIP-seq]

status: Public on Mar 07 2025

city: Hangzhou

first: Jiang

last: Penglei

address: Yuhangtang Road 866

department: School of basic medicine science

institute: Zhejiang University

summary: DNA methylation is a significant component in proximal chromatin regulation and plays crucial roles in regulating gene expression and maintaining the repressive state of retrotransposon elements. However, accurate profiling of the proteomics which simultaneously identifies specific DNA sequences and their associated epigenetic modifications remains a challenge. Here, we report SelectID, which introduced methylated DNA binding domain into dCas9-mediated proximity labeling system to enable in situ protein capture at repetitive elements with 5-methylcytosine (5mC) modifications. SelectID were demonstrated as feasible as dCas9-TurboID system at specific DNA methylation regions, such as the chromosome 9 satellite. Using SelectID, we successfully identified CHD4 as potential repressors of methylated LINE-1 retrotransposon through direct binding at the 5’UTR of young LINE-1 elements. Overall, our SelectID approach has opened up new avenues for uncovering potential regulators of specific DNA regions with DNA methylation, which will greatly facilitate future studies on epigenetic regulation.

overall_design: ChIP assays for dCas9 and MBD were conducted in Hela cells transfected with the SelectID cassettes targeting the Chr9 satellite region or L1 elements, using anti-MycTag and anti-Flag antibodies. CHD4 ChIP assays were performed in wild-type Hela cells using a CHD4 antibody. All experiments were carried out in duplicate.


title: Brain 5-hydroxymethylcytosine alterations are associated with Alzheimer’s disease neuropathology

city: Tampa

first: Jinying

last: Zhao

state: FL

address: 3650 Spectrum Blvd

institute: University of South Florida

summary: DNA 5-hydroxymethylcytosine (5hmC), also known as the sixth DNA base of the genome, plays an important role in neurogenerative disorders. However, little is known about its genome-wide distribution and its association with Alzheimer’s disease neuropathology. Here, we report a genome-wide profiling of 5hmC in 1,050 autopsied brains (dorsolateral prefrontal cortex) of older adults in the Religious Orders Study/Memory and Aging Project (ROSMAP) cohorts. This resource will facilitate future research of DNA methylation and demethylation in Alzheimer’s disease and other neurological disorders.

overall_design: We generated 5hmC profiles in 1,050 postmortem brain tissue samples who were part of the Religious Order Study (ROS) or the Rush Memory and Aging Project (MAP), collectively called ROSMAP. The 5hmC data was generated by hMe-Seal in a sample of dorsolateral prefrontal cortex (DLPFC) from each participant.

first: Peng

last: Jin

first: David

last: Bennett


title: Single-nuclei transcriptional and chromatin accessibility profile of Beckwith-Wiedemann Syndrome liver suggests metabolic dysregulation driven by PPARA signaling

city: Philadelphia

first: Jennifer

middle: Melissa

last: Kalish

state: PA

address: 3501 Civic Center Blvd, CTRB 3028

institute: Children's Hospital of Philadelphia

summary: Beckwith-Wiedemann Syndrome (BWS) is an epigenetic overgrowth syndrome caused by methylation changes in the human 11p15 chromosomal locus. Patients with BWS exhibit tissue overgrowth, as well as an increased risk of childhood neoplasms in the liver and kidney. To understand the new impact of these 11p15 changes, specifically in the liver, we performed single nucleus RNA sequencing (snRNA-seq) and single nucleus assay for transposase-accessible chromatin with sequencing (snATAC-seq) to generate paired, cell-type-specific transcriptional and chromatin accessibility profiles of both BWS-liver and nonBWS-liver nontumorous tissue. The integrated RNA+ATACseq multi-omic approach showed cell-type-specific enrichment and activation of the peroxisome proliferator-activated receptor ? (PPARA) – a liver metabolic regulator.  To confirm our findings, we utilized a BWS-induced pluripotent stem cell (iPSC) model, where cells were differentiated into hepatocytes. Our data demonstrates the dysregulation of lipid metabolism in BWS-liver, which coincided with observed upregulation of PPARA during hepatocyte differentiation. BWS liver cells exhibited decreased neutral lipids, increased fatty acid beta oxidation, and increased lipid peroxidation, relative to controls. Excess reactive oxygen species (ROS) induces lipid peroxidation and cellular DNA damage. This study proposes a potential mechanism for overgrowth and cancer predisposition in BWS liver due to perturbed metabolism.

overall_design: To validate PPARA as a altered pathway in BWS hepatocytes, we used engineered iPSCs that model BWS (3H5 and 3D1, referred to as BWS 1 and BWS 2) as well asunmodified normal parentaliPSCs(SV20, referred to as control)and differentiated them into iPSC-derived hepatocytes. We then profiled their expression using RNA-seq at three timepoints, Day 0, 15, and 20, with two biological replicates/timepoint.

first: Snehal

last: Nigude

first: Elisia

last: Tihy

first: Zhengfeng

last: Li

first: Rose

last: Prdieu

first: Mariah

last: Byne

first: Luis

middle: G

last: DeGomez

first: Brandon

last: Maou

first: Kathrin

middle: M

last: Bent

first: Wenli

last: Yag

first: Suzanne

last: MaFarland

first: Michael

last: Xi

last: Kaish


title: SMARTA CD4 T cells from spleen and lamina propria 8 days after infection with LCMV clone-13 on SPF, OMM12 and GF mice [scRNA-Seq 10x]

city: Freising

first: Gustavo

middle: P.

last: de Almeida

state: Bavaria

address: Liesel-Beckmann-Str. 1

department: Division of Animal Physiology and Immunology

institute: Technical University of Munich

summary: Comparison of the impact of specific microbiota on mouse CD4+ T cell response during chronic infection using scRNA-Seq.

overall_design: Specific pathogen free (SPF), oligo mouse microbiota12-colonized (OMM12), and germfree (GF) mice received 5000 adoptively transferred SMARTA T cells 5 days prior infection with LCMV Cl-13. SMARTA T cells (live/dead CD4+CD45.1+) cells from small intestine lamina propria and spleen were re-isolated at 8 dpi and subjected to single-cell RNAseq analysis.

first: Daphne

last: Kolland

first: Miriam

last: Kuhlmann

first: Dietmar

last: Zehn

first: Caspar

last: Ohnmacht


title: Insights into the stress response of Escherichia coli biofilms upon Plasma-activated water treatment.

city: Sydney

first: M. Mozammel

last: Hoque

state: NSW

address: 15 Broadway, Ultimo

department: Australian Institute for Microbiology & Infection (AIMI)

country: Australia

institute: University of Technology Sydney

summary: Biofilms on surfaces pose quality and health risks, resisting traditional antimicrobial methods. Plasma-activated water (PAW) shows promise in biofilm elimination, yet its genetic impact remains unclear. We investigated Escherichia coli biofilm responses to PAW treatment, revealing significant gene expression changes and pathway activations. Knockout mutants of key genes confirmed their role in PAW response. This study enhances our understanding of PAW's anti-biofilm mechanisms and bacterial stress responses.

overall_design: RNA-seq was performed to compare transcriptomes of Escherichia coli biofilm during in situ 2 min sub-lethal PAW treatment with and without superoxide (by adding the scavenger Tiron to remove it). Four independent biological replicates of 48 h ATCC 25922 E. coli biofilms were generated, each comprising four technical replicates were pooled. Pooled biofilms were treated in situ for 2 min with four different treatment solutions PAW, PAW-Tiron, Bubble, and Bubble-Tiron.

first: Heema

last: Vyas

first: M

first: Anne

last: Mai-Prochnow

first: Scott

last: Rice


title: Th1 polarization in Bordetella pertussis vaccine responses is maintained through a positive feedback loop

city: Amsterdam

first: Lisa

last: Willemsen

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC - locatie AMC

summary: Outbreaks of Bordetella pertussis (BP), the causative agent of whooping cough, continue despite broad vaccination coverage and have been increasing since vaccination switched from whole-BP (wP) to acellular BP (aP) vaccines. wP vaccination has been associated with more durable protective immunity and an induced Th1 polarized memory T cell response. Here, a multi-omics approach was applied to profile the immune response of 30 wP and 31 aP-primed individuals and identify correlates of T cell polarization before and after Tdap booster vaccination. We found that transcriptional changes indicating an interferon response on day 1 post-booster along with elevated plasma concentrations of IFN-γ and interferon-induced chemokines that peaked at day 1-3 post-booster correlated best with the Th1 polarization of the vaccine-induced memory T cell response on day 28. Our studies suggest that wP-primed individuals maintain their Th1 polarization through this early memory interferon response. This suggests that stimulating the interferon pathway during vaccination could be an effective strategy to elicit a predominant Th1 response in aP-primed individuals that protects better against infection.

overall_design: 2 million PBMC were lysed using QIAzol Lysis Reagent (Qiagen). Samples were stored at -80C until RNA extraction. RNA was extracted using the miRNeasy Mini Kit (Qiagen) including DNase treatment according to the manufacturer's instructions. The Smart-seq2 protocol was used to perform full-length bulkRNAseq. Briefly, RNA was captured using oligo-poly(dT)-30 primers and reverse transcription was performed using 50-template switching oligos (LNA technologies, Exicon). cDNA was pre-amplified using PCR and purified twice by magnetic beads (volume ratio 0.6x and 0.8x Ampure-XP magnetic beads, Beckman Coulter). cDNA was measured using capillary electrophoresis (Fragment analyzer, Advance analytical) and 0.5 ng of cDNA was used to generate indexed Illumina libraries (Nextera XT library preparation kit, Illumina). Each library's fragment size was measured by capillary electrophoresis (Fragment analyzer, Advance analytical) and was quantified (Picogreen, Thermofisher). Libraries were pooled at equal molar concentration and sequenced paired-end to a minimum depth of 15 million reads with each a length of 100 base pairs.

first: Jiyeun

last: Lee

first: Pramod

last: Shinde

first: Ferran

last: Soldevila

first: Minori

last: Aoki

first: Shelby

last: Orfield

first: Mari

last: Kojima

first: Ricardo

last: da Silva Antunes

first: Alessandro

last: Sette

first: Bjoern

last: Peters


title: Clinical evaluation of a functional combinatorial precision medicine platform to predict treatment outcomes and enhance combination therapy design in soft tissue sarcomas

status: Public on Mar 06 2025

city: Singapore

first: Xing Yi

last: Woo

address: 30 Biopolis Street #07-01 Matrix

country: Singapore

institute: Bioinformatics Institute, A*STAR

summary: Background Soft tissue sarcomas (STS) are a highly heterogeneous collection of tumors that arise from primitive mesenchymal cells. Survival outcomes for advanced STS patients remain poor, with effective agents limited primarily to cytotoxic chemotherapies, achieving responses below 15% as the standard of care. Although efforts to understand sarcomagenesis have identified potential biomarkers, the development of effective targeted therapies has been hindered by the diversity of STS subtypes and interpatient tumour heterogeneity. Given the uniquely individualized nature of STS, we hypothesized that the application of an ex vivo drug sensitivity platform, Quadratic Phenotypic Optimization Platform (QPOP), in primary STS patient samples can improve identification of effective drug regimens on a per-patient basis. In this study, we evaluated clinical concordance of QPOP to predict treatment outcomes in an STS cohort, and explored QPOP’s ranking function for drug combination discovery. Methods Freshly dissociated tumor samples were treated with a predesigned array of 155 test combinations to rank and compare all possible therapeutic combinations from a 12-drug set comprising STS standard of care, FDA approved drugs and promising investigational drugs. Concordance analysis was performed by comparing QPOP-defined outcomes with clinical outcomes from either QPOP-guided therapies or prior lines of treatment. Efficacy of the most frequently top-ranked drug combination was evaluated in both cell line and patient-derived models, and potential mechanisms were investigated using transcriptomic, ChIP-qPCR and in vivo studies. Results Across a total of 45 patient samples, QPOP demonstrated a total predictive value of 72.4% and an AUCROC of 74%, highlighting its discriminative ability in predicting treatment response in patients. We identified BETi and pazopanib as most frequently top-ranked in 67.8% of all patient samples, outperforming standard of care ifosfamide and doxorubicin. Validation in a panel of established patient lines and in vivo models supported its synergistic interaction, which shows repressed oncogenic MYC and related pathways. Conclusions Work here provides preliminary clinical evidence for QPOP to predict STS treatment outcomes and scientific rationale for an effective combinatorial therapeutic strategy validated in vivo that may offer new therapeutic options for sarcoma patients.

overall_design: To elucidate the underlying mechanisms of the potentiating effect observed in AZD5153 + pazopanib combination treatment, RNA-seq was performed on DDLPS cell line (LPS141) and established DDLPS patient-derived cells (PDC, hSC40), untreated, or treated with AZD5153 or pazopanib alone or in combination.

first: Brandon Xuan Ming

last: Phua

first: Sharon Pei Yi

last: Chan


title: A TGF-ß-induced cis-regulatory long non-coding RNA eSNAI1 activates SNAI1 enhancer and stimulates epithelial-to-mesenchymal transition of cancer cells [CRISPR screen, activation]

city: Solna

first: Bernhard

last: Schmierer

state: (optional)

address: Biomedicum 9B, Solnavagen 9

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

summary: Transforming growth factor-β (TGF-β) signaling stimulates cell movement and plasticity by inducing epithelial-to-mesenchymal transition (EMT). This process is aberrantly activated in cancer and facilitates tumor cell migration, invasion, metastasis, and therapy resistance. In this study, we identified the lncRNA eSNAI1 (SCREEM2) as a potent activator of TGF-β/SMAD signaling and SNAI1 expression. eSNAI1 depletion reduces TGF-β-induced EMT, migration, in vivo extravasation, stemness, and chemotherapy resistance of breast cancer cells. eSNAI1 promotes TGF-β/SMAD signaling by inhibiting TGF-β type I receptor polyubiquitination and proteasomal degradation. eSNAI1 stimulates the expression of the nearby gene SNAI1, which encodes the EMT transcription factor SNAI1 that facilitates TGF-β/SMAD signaling by retaining the inhibitory SMAD7 in the nucleus. Mechanistically, eSNAI1 acts as an enhancer RNA (eRNA) to potentiate SNAI1 expression through in-cis regulation. Furthermore, we uncovered that eSNAI1 interacts with and reinforces the binding of the co-activator bromodomain-containing protein 4 (BRD4) to the H3 lysine 27 acetylation (H3K27ac)-enriched SNAI1 enhancer region. Our findings identify eSNAI1 as a potent activator of TGF-β signaling and a promising therapeutic target to mitigate overactive TGF-β signaling and EMT in cancer cells.

overall_design: CRISPR-activation screen for a custom set of lncRNAs using the SAM system. MDA-MB231 expressing a TGFbeta inducible GFP reporter and dCas9-VP64 were transduced with a guide library. An early time point (ETP) control sample was taken at day 5 post-transduction. AT day 7 post transduction, cells were treated with TGF-beta for 24 hours. An unsorted control sample was taken, and the 15% highest and lowest GFP expressors were sorted. The screen was performed in two replicates

first: Chuannan

last: Fan

first: Qian

last: Wang

first: Peter

middle: H

last: Krijger

first: Davy

last: Cats

first: Miriam

last: Selle

first: Olga

last: Khorosjutina

first: Soniya

last: Dhanjal

first: Hailiang

last: Mei

first: Wouter

last: de Laat

last: ten Dijke


title: Effect of patient' serum of different timepoints on CD3 T cells at day 2 after in vitro cell culture

city: Hefei

first: Liang

state: Anhui

address: 96 Jinzhai Road

institute: University of Science and Technology of China

summary: To examine the impacts of these differences in recipients’ serum on donor T-cell activation

overall_design: we performed in vitro cell culture assays on T cells selected from PBMCs of healthy donor by adding patients’ peripheral serum collected at 7 am (7 am group) or 4 pm (4 pm group) for 2 days

first: Yue

last: Wu

first: Yiwen

last: Hou

first: Xiaoyu

last: Zhu

first: Cheng

last: Zhan


title: TSC2 loss in neural progenitor cells suppresses mRNA translation of neurodevelopmental genes

city: Stockholm

first: Krzysztof

middle: Jan

last: Szkop

state: Solna

address: SciLifeLab, Tomtebodavägen 23

department: Department of Oncology and Pathology

summary: Tuberous sclerosis complex (TSC) is an inherited neurodevelopmental (ND) disorder with frequent manifestations of epilepsy and autism spectrum disorder (ASD) caused by mutations in TSC1 or TSC2 genes. TSC1 and TSC2 form a complex inhibiting mechanistic target of rapamycin complex-1 (mTORC1) signaling, leading to hyperactive mTORC1 signaling upon TSC1/2 loss of function. Although rapalogs, which are FDA-approved allosteric mTORC1-selective inhibitors, are used to treat TSC-associated hamartomas, they are not effective for treating ND manifestations. mTORC1 signaling controls protein synthesis by regulating formation of the eIF4F complex, whose activity is further modulated by the MNK1/2 kinases via phosphorylation of the eIF4F subunit eIF4E. While both these pathways modulate translation in transcript-selective fashion depending on features in target mRNAs’ 5’ untranslated regions (5’UTRs), their effect on transcriptome-wide patterns of mRNA translation has not been compared. Here, employing CRISPR-modified, isogenic TSC2 patient-derived neural progenitor cells (NPCs), we examined how loss of TSC2 affects gene expression via changes in mRNA abundance and translation at a transcriptome-wide scale. This revealed abundant mRNA translation alterations in TSC2-Null NPCs overlapping with those we previously observed in TSC1-Null NPCs. Surprisingly, numerous non-monogenic ASD- and NDD-associated genes, identified in patients harboring putative loss-of-function mutations, were selectively translationally suppressed in TSC2-Null NPCs consistent with their distinct repertoire of 5’UTR features. Importantly, translation of these ASD- and NDD-associated genes was reversed upon inhibition of either mTORC1 or MNK1/2 signaling using RMC-6272 or eFT-508, respectively. This study thereby establishes mTORC1-eIF4F and MNK-eIF4E-sensitive mRNA translation as key components in TSC, ASD and other neurodevelopmental disorders; and lay the groundwork for evaluating drugs in clinical development that target these pathways as a treatment strategy for TSC as well as ASD/NDD.

overall_design: Analysis of total and polysomal mRNA samples of NPCs derived from a female TSC2 patient, including TSC2-null (-/-) and CRISPR-corrected TSC2-WT (+/+), treated with DMSO or mTOR1 signaling inhibitor RMC-6272 or MNK1/2 signaling inhibitor eFT-508.

first: Pauline

last: Martin

first: Francis

last: Robert

first: Srirupa

last: Bhattacharyya

first: Roberta

last: Beauchamp

first: Jacob

last: Brenner

first: Nicholas

last: Redmond

first: Sidong

last: Huang

first: Serkan

last: Erdin

first: Ola

last: Larsson

first: Vijaya

last: Ramesh


title: Identification of a SNAI1 enhancer RNA that drives cancer cell plasticity

city: Utrecht

first: Peter

last: Krijger

address: Uppsalalaan 8

institute: Hubrecht Institute

summary: Enhancer RNAs (eRNAs) are a pivotal class of enhancer-derived non-coding RNAs that drive gene expression. Here we identify the SNAI1 enhancer RNA (SNAI1e; SCREEM2) as a key activator of SNAI1 expression and a potent enforcer of transforming growth factor-β (TGF-β)/SMAD signaling in cancer cells. SNAI1e depletion impairs TGF-β-induced epithelial-mesenchymal transition (EMT), migration, in vivo extravasation, stemness, and chemotherapy resistance in breast cancer cells. SNAI1e functions as an eRNA to cis-regulate SNAI1 enhancer activity by binding to and strengthening the enrichment of the transcriptional co-activator bromodomain-containing protein 4 (BRD4) at the local enhancer. SNAI1e selectively promotes the expression of SNAI1, which encodes the EMT transcription factor SNAI1. Furthermore, we reveal that SNAI1 interacts with and anchors the inhibitory SMAD7 in the nucleus, and thereby prevents TGF-β type I receptor (TβRI) polyubiquitination and proteasomal degradation. Our findings establish SNAI1e as a critical driver of SNAI1 expression and TGF-β-induced cell plasticity.

overall_design: 4C-seq data with a VP located at eSNAI1 in MDA-MB-231 cells treated with or without TGFb.

first: Chuannan

last: Fan

first: Qian

last: Wang

first: Davy

last: Cats

first: Hailiang

last: Mei

first: Bernhard

last: Schmierer

first: Wouter

last: de Laat


title: iPSC data for the paper "Correction of dysregulated lipid metabolism normalizes gene expression in oligodendrocytes and prolongs lifespan in female poly-GA C9orf72 mouse model"

city: Munich

first: Ali

last: Rezaei

summary: These sequences support the following paper abstract: Clinical and genetic research links altered cholesterol metabolism with ALS development and progression, yet pinpointing specific pathomechanisms remain challenging. We investigated how cholesterol dysmetabolism interacts with protein aggregation, demyelination, and neuronal loss in ALS. Bulk RNAseq transcriptomics showed decreased cholesterol biosynthesis and increased cholesterol export in ALS mouse models (GA-Nes, GA-CFP, rNLS8) and patient samples (spinal cord), suggesting an adaptive response to cholesterol overload. Consequently, we assessed the efficacy of the cholesterol-binding drug 2-hydroxypropyl-β-cyclodextrin (CD) in a fast-progressing C9orf72 ALS mouse model with extensive poly-GA expression and myelination deficits. CD treatment normalized cholesteryl ester levels, lowered neurofilament light chain levels, and prolonged lifespan in female but not male GA-Nes mice, without impacting poly-GA aggregates. Single nucleus transcriptomics indicated that CD primarily affected oligodendrocytes, significantly restored myelin gene expression, increased density of myelinated axons, inhibited the disease-associated oligodendrocyte response, and downregulated the lipid-associated genes Plin4 and ApoD. These results suggest that reducing excess free cholesterol in the CNS could be a viable ALS treatment strategy.

overall_design: RNAseq profiling of iPSC-derived neurons (human neurons were generated by doxycycline-mediated induction of NGN2 expression in small neural precursor cells (smNPC)) transduced with GFP or poly(GA). The neurons were then treated with HPbCD (referred to as "CD") or vehicle (referred to as "ctrl") for 19 days, with treatment occurring every other day.

first: Virág

last: Kocsis-Jutka

first: Zeynep

middle: I

last: Gunes

first: Qing

last: Zeng

first: Georg

last: Kislinger

first: Franz

last: Bauernschmitt

first: Huseyin

middle: B

last: Isilgan

first: Laura

middle: R

last: Parisi

first: Tuğberk

last: Kaya

first: Sören

last: Franzenburg

first: Jonas

last: Koppenbrink

first: Julia

last: Knogler

first: Thomas

last: Arzberger

first: Daniel

last: Farny

first: Brigitte

last: Nuscher

first: Eszter

last: Katona

first: Chao

last: Yang

first: Garyfallia

last: Gouna

first: Qihui

last: Zhou

first: Nellwyn

last: Hagan

first: Dimitry

last: Ofengeim

first: Eduardo

last: Beltrán

first: Οzgun

last: Gokce

first: Mikael

last: Simons

first: Sabine

last: Liebscher

first: Dieter

last: Edbauer


title: Transcriptomic analysis for temporomandibular joint arthritis

city: Sharjah

first: Rifat

last: Hamoudi

state: Sharjah

address: M32 Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, , Sharjah

department: Clinical Sciences

country: United Arab Emirates

institute: University of Sharjah

summary: Background: Temporomandibular joint osteoarthritis (TMJOA) is a degenerative disease marked by the progressive degeneration of cartilage and underlying bone, resulting in pain and functional impairment. Despite current conservative treatments such as physical therapy and NSAIDs, the etiology and pathophysiology of TMJOA are unclear, making effective management difficult. Finding reliable biomarkers for early identification and new therapeutic targets is crucial to improve treatment outcomes.

overall_design:
Methods: The goal of this study was to identify possible salivary biomarkers for TMJ-OA through an integrative strategy that included both in silico  and clinical validation. Transcriptomic data from the Gene Expression Omnibus (GEO) dataset GSE205389 were analysed to identify differentially expressed genes (DEGs) in TMJ-OA patients versus healthy controls. RNA sequencing was carried out on saliva samples from both group, TMJ-OA patients and healthy controls. DEGs were validated with quantitative reverse transcription PCR (qRT-PCR). Gene set enrichment analysis (GSEA) and pathway annotation tools such as Metascape were used to uncover biological pathways linked to TMJ-OA.
Results: In silico analysis revealed 81 differentially active pathways, with 3554 DEGs substantially associated with TMJOA. Among the top 20 DEGs, CRIP1, PPA1, TARS1 and GCLC were significantly increased in TMJ-OA patients compared to controls. These genes were engaged in inflammation, metabolic processes, and oxidative stress, indicating a role in illness progression. Actin filament polymerization, osteoclast differentiation, and immune regulatory pathways were shown to be significantly enriched.
Conclusion: This work reveals CRIP1, PPA1,TARS1 and GCLC as possible salivary biomarkers for TMJ-OA, offering novel insights into disease pathophysiology. The findings imply that these genes could be used as diagnostic markers and therapeutic targets for TMJ-OA, particularly in the Arabic population. Additional large-scale research is required to confirm these biomarkers and investigate targeted therapies for illness management.
Temporomandibular joint osteoarthritis (TMJOA) and healthy control

first: Nawal

last: Alketbi

first: Alaa

last: Altaie

first: Reem

middle: S

last: Alhamidi

first: Mohamed

last: Haider

first: Wael

last: Talaat


title: Identification of a unique subset of group 3 innate lymphoid cells in the lung vasculature of mice

city: New York

first: Yuefeng

last: Huang

state: NY

address: 701W 168th Street

department: Microbiology & Immunology

institute: Columbia University

summary: Bulk RNA-sequencing of distinct ILC3 subpopulations sorted from murine lungs during steady state and bacterial infection.

overall_design:
To investigate the functions of vILC3s and tILC3s, these cell subsets were sorted from the lungs of RORgt-eGFP report mice, based on their expression of RORgt-eGFP at steady state or from mice infected with Pseudomonas aeruginosa for 72 hours.
We performed gene expression profiling analysis using data obtained from RNA-seq of vILC3s and tILC3s, at steady state (no treatment (NT)) and from the lungs mice at 72 hours post-infection with Pseudomonas aeruginosa (Pa).
Comparative gene expression profiling analysis of RNA-seq data for NT vILC3 vs NT tILC3s, Pa vILC3 vs Pa tILC3s, NT vILC3 vs Pa vILC3, and NT tILC3 vs Pa tILC3s.

first: Jiacheng

last: Jin

first: Wanwei

last: Zhang

first: Simon

last: Shirley


title: The network response to Egf is tissue-specific

city: Boston

first: Kevin

last: Haigis

state: MA

address: 450 Brookline Avenue, LC 8303

institute: Dana Farber Cancer Institute

summary: Epidermal growth factor receptor (EGFR)-driven signaling regulates fundamental cellular processes. Dysregulated signaling via EGFR is implicated in numerous disease pathologies, and distinct EGFR-associated disease etiologies are known to be tissue-specific. The molecular basis of this tissue specificity remains poorly understood. Most studies of EGFR signaling to date have been performed in vitro or in tissue-specific mouse models of disease, which has limited insight into EGFR signaling patterns in healthy tissues. Here, we carried out integrated phosphoproteomic, proteomic, and transcriptomic analyses of signaling changes across various mouse tissues in response to short-term stimulation with the Egfr ligand Egf. We show how both baseline and Egf-stimulated signaling behaviors differ between tissues. Moreover, we propose how baseline phosphorylation and total protein levels may be associated with clinically relevant tissue-specific Egfr-associated phenotypes. Altogether, our analyses illustrate tissue-specific effects of Egf stimulation and highlight potential links between underlying tissue biology and Egfr signaling output.

overall_design: Wild-type C57BL/6J mice (female, 10-wk-old) were retro-orbitally injected with either 1 mg/kg Egf dissolved in PBS or an equivalent volume of PBS. Heart, lung, kidney, and liver were collected for gene expression analysis at 2 or 6 hours following treatment. Three additional untreated mice were used as controls.


title: A TGF-β-induced long non-coding RNA eSNAI1 activates SNAI1 enhancer in cis and stimulates epithelial to mesenchymal transition of cancer cells

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

institute: Leiden University Medical Center

summary: We identified a tumor-promoting long non-coding RNA (lncRNA) named eSNAI1 (enhancer RNA of SNAI1) which is induced by TGF-beta and enforces TGF-beta signaling. It was found to promtotes TGF-beta-induced epithelial-to-mesenchymal transition (EMT), cell migration and extravasation in a zebrafish exnograft model. To better dissect the downstream target genes and elucidate the signaling pathways altered by eSNAI1, we overexpressed eSNAI1 by CRISPRa in MDA-MB-231 cells. Total RNA was collected and sent for RNA sequencing analysis. Afterwards, differentially expressd genes were used for the pathway enrichment analysis and gene set enrichment analysis (GSEA).

overall_design: eSNAI1 is overexpressed by a CRISPRa system with two independent gRNAs in MDA-MB-231 cells. RNA from cells transduced with the empty vector for gRNA expression was set as a control. Three biological replicates were included in each group.

first: Chuannan

last: Fan

first: Peter

last: ten Dijke


title: Human exosomes deliver small RNAs into bacteria and silence bacterial genes

city: Nanjing

first: Chen

last: Wang

state: Jiangsu

address: 163 Xianlin Avenue

department: Life Sciences

institute: Nanjing University

type: Non-coding RNA profiling by high throughput sequencing

summary: Humans and microorganisms, both symbiotic and pathogenic, have evolved means to communicate through the dissemination of biological signals. In addition to small molecules and proteins, mobile small RNAs (sRNAs) have recently emerged as signal molecules that mediate inter-species crosstalk by functional RNA interference (RNAi). However, the trafficking of sRNAs between humans and microorganisms, as well as the resulting biological consequences, remains unexplored. Here, we report that human cells secrete exosomes to deliver sRNAs into bacteria and induce bacterial gene silencing. The unprecedented RNAi in bacteria is accomplished primarily through translational repression without mRNA degradation, for which the participation of human AGO2 proteins co-transferred with sRNAs is essential. Exosome-mediated bacterial RNAi was further applied to fight superbug infection by targeting drug-resistance genes in a mouse model. Our discovery of this unique exosome-mediated sRNA delivery and gene silencing in bacteria paves the way to understanding and manipulating the cross-kingdom communication between human hosts and intestinal microbiota, as well as between humans and pathogenic bacteria.

sample_organism:
Escherichia coli
Staphylococcus aureus
Homo sapiens

overall_design: Fresh samples were prepared and stored at -80℃. Total RNA from exosomes and bacteria were extracted and solexa sequencing was performed.

first: Wangjian

last: Sheng

first: Yu

last: Zhou

first: Chen-Yu

first: Huan


title: ADAT3 variants disrupt the activity of the ADAT tRNA deaminase complex and impair neuronal migration.

status: Public on Mar 05 2025

city: Martinsried

first: Danny

last: Nedialkova

address: Am Klopferspitz 18

institute: Max Planck Institute of Biochemistry

summary: The ADAT2/ADAT3 (ADAT) complex catalyzes the adenosine to inosine modification at the wobble position of eukaryotic tRNAs. Mutations in ADAT3, the catalytically inactive subunit of the ADAT2/ADAT3 complex, have been identified in patients presenting with severe neurodevelopmental disorders. Yet, the physiological function of ADAT2/ADAT3 complex during brain development remains totally unknown. Here, we investigated the role of the ADAT2/ADAT3 complex in cortical development. First, we reported 21 new neurodevelopmental disorders patients carrying biallelic variants in ADAT3. Second, we used structural, biochemical, and enzymatic assays to deeply characterized the impact of those variants on ADAT2/ADAT3 structure, biochemical properties, enzymatic activity and tRNAs editing and abundance. Finally, in vivo complementation assays were performed to correlate functional deficits with neuronal migration defects in the developing mouse cortex. Our results showed that maintaining a proper level of ADAT2/ADAT3 catalytic activity is essential for radial migration of projection neurons in the developing mouse cortex. We demonstrated that the identified ADAT3 variants significantly impaired the abundance and, for some, the activity of the complex, leading to a substantial decrease in I34 levels with direct consequence on their steady-state. We correlated the severity of the migration phenotype with the degree of the loss of function caused by the variants. Altogether, our results highlight the critical role of ADAT2/ADAT3 during cortical development and provide cellular and molecular insights into the pathogenic mechanisms underlying ADAT3-related neurodevelopmental disorders.

overall_design: tRNA-seq datasets were generated from human lymphoblastoid cell lines (LCLs) from patients and healthy controls to investigate the impact of biallelic variants in ADAT3 on tRNA abundance and aminoacylation.

first: Till

last: Balla

middle: D

first: Juliette

last: Godin


title: Hmgb2 improves astrocyte to neuron conversion by increasing the chromatin accessibility of genes associated with neuronal maturation in a proneuronal factor-dependent manner[RNA-Seq]

city: Planegg-Martinsried

first: Jovica

last: Ninkovic

address: Großhaderner Straße 9

department: Department of Cell Biology and Anatomy III

institute: Biomedical Center (BMC),LMU - Munich

summary: Direct conversion of reactive glial cells to neurons is promising avenue for the replacement therapies after brain injury or neurodegeneration. The overexpression of developmental neurogenic fate determinants in glial cells converts them to neurons. For the repair purposes the conversion is confined to the pathology-induced neuroinflammatory environment. However, very little is known about the influence of injury-induced neuroinflammatory environment on the direct conversion process. We established the new in vitro culture system of postnatal astrocytes that reflects the direct conversion rate in the injured, neuroinflammatory environment in vivo. We could show that the growth factor combination corresponding to the injured environment defines the capacity of the glia to be directly converted to neurons. Using this culture, we showed that the chromatin structural protein high mobility group b2 (Hmgb2) regulates the direct conversion rate downstream of the growth factor combination. We could further show that Hmgb2 cooperates  with neurogenic fate determinants such as Neurog2 to open the chromatin containing neuronal maturation and synapse formation genes, leading to early chromatin re-arrangements during the direct fate conversion that are necessary for the full fate conversion. Our data demonstrate the novel, environmental cues controlled level of gene regulation during direct fate conversion necessary for the proper maturation of induced neurons that could be targeted to improve the repair process.

overall_design: To investigate the role of Hmgb2 in direct astroglia to neuron conversion, we infected glial cells from postnatal mice (P6-P8, gray matter) with retroviral vectors encoding Hmgb2, Neurog2, both, or GFP as a control. After 48 hours of infection, we purified the cells using fluorescence-activated cell sorting (FACS) and performed RNA-Seq and ATAC-Seq on the sorted cells to analyze the transcriptomic and chromatin accessibility profiles of the cells.

first: Priya

last: Maddhesiya

first: Tjasa

last: Lepko

first: Andrea

last: Steiner-Mezzardi

first: Veronika

last: Schwarz

first: Juliane

last: Merl-Pham

first: Finja

last: Berger

first: Stefanie

last: Hauck

first: Lorenza

last: Ronfani

first: Giacomo

last: Massadotti

first: Magdalena

last: Götz


title: Ectopic germinal centers in the nasal turbinates contribute to B cell immunity to intranasal viral infection and vaccination

city: Goteborg

first: Davide

last: Angeletti

address: Medicinaregatan 7a

institute: University of Gothenburg

summary: The nasal mucosa is the first immunologically active site that respiratory viruses encounter and establishing immunity at the initial point of pathogen contact is essential for preventing viral spread. Influenza A virus (IAV) in humans preferentially replicates in the upper respiratory tract (URT) but mouse models of infection result in lower respiratory tract (LRT) infection. Here we optimize IAV inoculation to enhance replication in the nasal turbinate (NT) and study local B cell immunity. We demonstrate that URT-targeted IAV infection stimulates robust local B cell responses, including germinal centre (GC) B cell formation in the NT, outside of classical nasal associated lymphoid tissues (NALT). NT GC contribute to local tissue resident B cell generation and enhance local antibody production. Furthermore, URT-focused immunization also induces significant GC formation in the NT.  Finally, we detect steady-state GC in the NT of both mice and healthy humans, suggesting continuous immune surveillance triggered by environmental stimuli. These findings highlight the pivotal role of the NT in local and systemic immunity, with important implications for future mucosal vaccines targeting the upper airways.

overall_design: Here we have infected mice with IAV-PR8 and sacrificed them at 21 days after infection.  we collected nasal tissue (NT), NALT and cervical LN from 8 males S1pr2CreERT2-tdTomato mice, treated daily with Tamoxifen. Sorting on GC B cells  (B220+ GL7+ IgD- CD38-) TdTomato+ . each organ was hashtagged individually and pooled

first: Gailleton

last: Romain

first: Mathew

last: Nimitha

first: Reusch

last: Laura

first: Schön

last: Karin

first: Scharf

last: Lydia

first: Strömberg

last: Anneli

first: Cvjetkovic

last: Andrea

first: Aziz

last: Luaay

first: Hellgren

last: Johan

first: Bemark

last: Mats

first: Tang

last: Ka-Wei

first: Angeletti

last: Davide


title: Hmgb2 improves astrocyte to neuron conversion by increasing the chromatin accessibility of genes associated with neuronal maturation in a proneuronal factor-dependent manner

first: Jovica

last: Ninkovic

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

overall_design: Refer to individual Series


title: Blood RNA transcripts show changes in inflammation and lipid metabolism in Alzheimer’s disease and mitochondrial function in mild cognitive impairment

city: Toon

first: Junichi

last: Iga

state: Ehime

address: Shitsukawa 454

department: Neuropsychiatry

institute: Ehime University

summary: Abnormal immunity in the periphery appears to be involved in the pathogenesis of Alzheimer’s disease (AD). In this study, blood transcriptome analyses of patients with AD, those with mild cognitive impairment (MCI) due to AD, and heathy controls were performed to elucidate immune-mediated pathophysiology. The sample included 63 subjects from the Nakayama Study who were clinically diagnosed as (1) healthy controls (N=21), (2) having MCI due to AD (N=20), and (3) having AD (N=21). Blood samples were taken, magnetic resonance imaging was performed, and questionnaires were administered. RNA-seq, differential gene expression, gene ontology, pathway enrichment, and ingenuity pathway analyses were conducted, and polymerase chain reaction testing was performed. The results showed that neutrophil extracellular trap signaling was increased, and lipid metabolism (FXR/RXR activation, triacylglycerol degradation) was decreased in AD, whereas MCI showed protective responses via decreased neutrophil extracellular trap signaling and mitochondrial functions such as upregulation of the sirtuin pathway and downregulation of oxidative stress. Based on these findings, immune cells appear to have important roles in the pathogenesis of AD, and the transcriptome in blood may be useful as a biomarker for diagnosis via monitoring immunity in MCI and AD.

first: Jun-ichi


title: Hmgb2 improves astrocyte to neuron conversion by increasing the chromatin accessibility of genes associated with neuronal maturation in a proneuronal factor-dependent manner [ATAC-Seq]

first: Priya

last: Maddhesiya

first: Tjasa

last: Lepko

first: Andrea

last: Steiner-Mezzardi

first: Veronika

last: Schwarz

first: Juliane

last: Merl-Pham

first: Finja

last: Berger

first: Stefanie

last: Hauck

first: Lorenza

last: Ronfani

first: Giacomo

last: Massadotti

first: Magdalena


title: The sperm quality in DIO male mice is linked to the NF-κB signaling and Ppp2ca expression in the hypothalamus

city: NanJing

first: Xu

last: Feng

address: 101 Long Mian avenue

institute: Nanjing Medical University

summary: Emerging studies have reported a significant correlation between obesity and a decline in sperm quality among males, however, the underlying mechanism remains elusive. In this study, we observed that male mice with diet-induced obesity (DIO) exhibited functional alteration in the hypothalamic-pituitary-gonadal (HPG) axis, as evidenced by disruption of luteinizing hormone (LH) pulse release. This alteration was attributed to the activation of nuclear factor kappa B subunit (NF-κB) signaling in the hypothalamus, which subsequently led to a decline in sperm quality. The application of RNA-seq analysis in the hypothalamic arcuate nucleus (ARC) of DIO male mice has revealed a signaling network implicating protein phosphatase 2 catalytic subunit alpha (Ppp2ca), which is involved in the disruption of LH pulse secretion. Activation of NF-κB signaling increased expression, which decreased the Kiss1 expression through inhibition of Akt kinase (AKT) and cAMP responsive element binding protein 1 (CREB1) activities. Overexpression of the Ppp2ca gene in the hypothalamic ARC resulted in disrupted LH pulse secretion patterns and reduced sperm quality. Collectively, our findings provide novel insights into the molecular mechanisms underlying the decline in sperm quality observed in male DIO mice.

overall_design: Four weeks old male mice were fed either an ordinary diet (NCD; 16.5% fat, cobio, catalog No:1010086) or a high-fat diet (HFD; 60% fat, Research Diets, catalog No: D12492) for 16 weeks. Mouse body weight was measured every week.The brains of mice were harvested and thoroughly washed in cold PBS solution until complete removal of any residual blood on their surfaces was achieved. Subsequently, they were preserved by embedding them in OCT compound and storing them at -80℃. Brain tissue sections measuring 20 μm thickness were obtained using a Microtome Cryostat (Thermo, America). These sections were securely mounted onto slides coated with laser microcut membrane (Leica, 11505190). A laser microdissection system (Leica, Germany) was employed to precise excision ARC regions within the brain sections. The harvest tissues were collected into a RNase-free tube and storage at -80℃.


title: Host responses to S. pneumoniae in wild type and Mertk mutant mice II

status: Public on Mar 04 2025

city: Chapel Hill

first: Matthew

last: McPeek

state: NC

address: 125 Mason Farm Rd. CB:7248

institute: University of North Carolina

summary: Streptococcus pneumoniae is the leading cause of community-acquired pneumonia. Mertk is an efferocytosis receptor involved in the recognition and removal of apoptotic debris by macrophages and other phagocytic cells. Here we show that Mertk negatively regulates the clearance of S. pneumoniae, as measured by the greater number of viable bacteria in the lung of wild type vs. Mertk-/- mice 24 hours post-inoculation. The impaired clearance observed in wild type mice was associated with a greater number of neutrophils in the bronchoalveolar lavage (BAL) and lower concentration of IFNγ in the BAL fluid; however, similar enhancement of clearance was observed in Mertk-/- mice receiving neutralizing IFNγ antibody. Mertk is highly expressed on alveolar macrophages. Transcriptomic changes observed in primary Mertk-/- alveolar macrophages were associated with leukocyte activation, cellular motility, and response to stimulus. Mertk deficiency similarly enhanced proinflammatory gene expression in S. pneumoniae-stimulated alveolar macrophages in vitro and in pneumonic lung tissue. Thus, Mertk contributes to alveolar macrophage homeostasis through the receptor’s immunomodulatory role. Naive Mertk-/- alveolar macrophages appear primed for an inflammatory response to S. pneumoniae leading to greater cell motility, improved bacterial killing and enhancement of other innate immune cells through the production of inflammatory mediators.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for cultured, primary alveolar macrophages isolated from Mertk-/- or wild type mice stimulated with Streptococcus pneumoniae or medium (unstimulated) for 4 hours.

first: Claire

last: Doerschuk


title: Single-Cell Transcriptomic Profiling of the Tumor Microenvironment in Treatment-Naive Hepatocellular Carcinoma Patients

status: Public on Mar 03 2025

city: changsha

first: Muqi

last: Liu

state: Hunan

address: No.138 Tongzipo Road, Yuelu District, Changsha

department: Institute for Cell Transplantation and Gene Therapy

institute: the 3rd Xiangya Hospital of Central South University

summary: This study provides high-resolution single-cell RNA sequencing (scRNA-seq) data of tumor tissues from 12 treatment-naive hepatocellular carcinoma (HCC) patients. The dataset captures the transcriptomic profiles of diverse cell populations, including tumor cells, immune cells (e.g., T cells, B cells, macrophages), and stromal cells, revealing cellular heterogeneity and key gene expression signatures within the HCC tumor microenvironment (TME). This resource is critical for investigating HCC pathogenesis, identifying therapeutic targets, and developing immunotherapeutic strategies.

overall_design: Samples: Fresh tumor tissues from 12 treatment-naive HCC patients with no prior surgery, chemotherapy, or radiotherapy,surgical puncture sample.  Single-cell preparation: Tissues were dissociated via mechanical disruption and enzymatic digestion, followed by fluorescence-activated cell sorting (FACS) or microfluidics to obtain high-quality single-cell suspensions.  Sequencing platform: Libraries were constructed using the 10x Genomics Chromium system and sequenced on Illumina NovaSeq 6000 (paired-end 150 bp).  Data analysis: Raw data processed via Cell Ranger pipeline for alignment and gene quantification; Seurat/R packages for cell clustering, annotation, and differential expression analysis. Cell subsets were annotated using canonical markers (e.g., EPCAM, CD3E, CD79A, CD68).  Quality control: Low-quality cells (genes <200 or mitochondrial gene ratio >20%) were excluded.

first: Wei

last: Wang

first: Qi

last: Liang

first: Xiaoqian

last: Ma

first: muqi


city: Lund

first: Johan

last: Staaf

address: Medicon Village

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

type: Methylation profiling by genome tiling array

summary:
DNA methylation profiling of TNBC primary tumors (surgically resected) to validate DNA methylation epitypes. Illumina EPIC V1 set
DNA methylation profiling of TNBC primary tumors (surgically resected) to validate DNA methylation epitypes. Illumina EPIC V2 set (GSM8826913-GSM8826971).

overall_design:
DNA methylation of tumor DNA was performed using Illumina MethylationEPIC V1 beadchips on 77 tumors according to manufacturer's instructions. No replicates.
DNA methylation of tumor DNA was performed using Illumina MethylationEPIC V2 beadchips on 59 tumors according to manufacturer's instructions. No replicates (GSM8826913-GSM8826971)
========================
Submitters state "Due to Swedish law we are not allowed to openly deposit any data that can be considered personal patient information. The EPIC platform contains non CpGs, therefore we cannot deposit IDAT files. We have prepared matrix files including only cg probes (CpG)s."
========================

last: Vallon-Christersson


title: Host responses to S. pneumoniae in wild type and Mertk mutant mice I

overall_design: Comparative gene expression profiling analysis of RNA-seq data for naive, primary alveolar macrophages isolated from Mertk-/- or wild type mice.


title: Host responses to S. pneumoniae in wild type and Mertk mutant mice III

overall_design: Comparative gene expression profiling analysis of RNA-seq data for naïve and pneumonic (24 hour Streptococcus pneumoniae) left lung tissue isolated from Mertk-/- or wild type mice.


title: Harnessing STING Signaling and Natural Killer Cells to overcome PARP Inhibitor Resistance in Homologous Recombination Repair altered Breast Cancer [scTCR-Seq]

city: Barcelona

first: Lara

last: Nonell

address: C/ NATZARET, 115-117

department: VHIOinformatics

country: Spain

institute: Vall d'Hebron Institute of Oncology (VHIO)

summary: Homologous recombination deficiency (HRD) contributes to genomic instability and leads to sensitivity to poly ADP-ribose polymerase inhibitors (PARPi). HRD also activates the cyclic GMP–AMP synthase (cGAS)-STimulator of INterferon Genes (STING)-Interferon (IFN) pathway, highlighting the need to understand the impact of cGAS-STING-IFN signaling on PARPi efficacy. In this study, we analyzed a cohort of thirty-five breast cancer (BC) patient-derived xenografts (PDX) and mouse-derived allografts (MDA). PARPi sensitivity correlated with HRD, increased genomic instability, and activation of the cGAS-STING-IFN signaling pathway. Single-cell analyses showed that IFN signaling and IFN-based immune interactions were suppressed in preclinical models with acquired resistance to PARPi, lacking concomitant clonal expansion of functional CD8+ T cells. However, the combination of PARPi and a novel STING agonist (STINGa) increased immune infiltration and resulted in superior antitumor activity in these tumors. Notably, the efficacy of PARPi monotherapy and the combination treatment with a STINGa was dependent on Natural Killer (NK) cells. In agreement, BC patients with BRCA1/BRCA2 mutations and good responses to PARPi showed higher abundancy of CD56+ NK cells in the tumor microenvironment and treatment-engaged CD56bright NK cells in the peripheral immune compartment, compared to those with poor responses. Therefore, these findings propose the combination of PARPi and STINGa as a potential novel strategy to enhance the therapeutic response in patients with acquired PARPi resistance and highlight a pivotal role of NK cells in the PARPi antitumor activity.

overall_design: We employed single-cell RNA-sequencing (scRNA-seq) combined with single-cell T cell receptor (TCR) sequencing (scTCR-seq) to analyze in depth the PARPi-induced immune response. PARPi-sensitive (MDA594) and PARPi-resistant (MDA594OR1)tumors derived from MDA594 were treated with olaparib or vehicle and processed in single-cell suspensions and sequenced with the 10x Genomics 5’ protocol.

first: Flaminia

last: Pedretti

first: Violeta

last: Serra


title: Harnessing STING Signaling and Natural Killer Cells to overcome PARP Inhibitor Resistance in Homologous Recombination Repair altered Breast Cancer [scRNA-seq]


title: A novel butyrate derivative, zinc dibutyroyllysinate, blunts MITF expression and up-regulates retinol and differentiation pathway mRNAs in a full-thickness human skin model

city: Dallas

first: William

last: Swindell

state: TX

address: 6201 Harry Hines Blvd

department: Internal Medicine

institute: UT Southwestern Medical Center

summary: Lysine, butyric acid and zinc play important roles in skin homeostasis that involve aging, inflam-mation and prevention of skin barrier disruption. This bioactivity spectrum is not replicated by any one topical compound currently in use. Our purpose in this study was to characterize a novel compound, zinc dibutyroyllysinate (ZDL), consisting of zinc with lysine and butyric acid moieties. We used RNA-seq to evaluate its effect on gene expression in a full-thickness skin model. We show that lysine alone has minimal effects on gene expression, whereas ZDL had greater transcriptional bioactivity. Effects of ZDL included increased expression of genes promoting epidermal differenti-ation and retinol metabolism, along with decreased expression of microphthalmia-associated transcription factor (MITF) and other melanogenesis genes. These effects were not replicated by an alternative salt compound (i.e., calcium dibutyroyllysinate). ZDL additionally led to a dose-dependent increase of extracellular matrix proteins in skin fibroblasts, including collagen I, collagen IV and prolidase. Loss of melanin secretion was also seen in ZDL-treated melanocytes. These results provide an initial characterization of ZDL as a novel topical agent. Our findings support a rationale for development of ZDL as a skincare ingredient, with potential applications for diverse conditions involving melanocyte hyperactivity, pigmentation, inflammation, or aging.

overall_design: Gene expression profiling experiments were carried out using EpiDermFT tissues (MatTek, Ashland, MA; cat no. EFT-400). The experiment included 4 treatments, in-cluding control (CTL), lysine (LYS), zinc dibutyroyllysinate (ZDL) and calcium dibu-tyroyllysinate (CDL) (n = 3 replicates/treatments).

first: Krzysztof

last: Bojanowski

first: Geovani

last: Quijas

first: Ratan

last: Chaudhuri


title: Doxorubicin induces the senescence-associated secretion phenotype in RAW264.7 cells

city: Shanghai

first: Heng

state: Shanghai

address: No.1630, Dongfang Road, Pudong New District, Shanghai, China.

department: Cardiovascular Surgery

institute: Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital

summary: Doxorubicin is a widely used anti-cancer drug, and its toxicological effects on healthy tissues, especially the heart, remains challenging in therapy. To explore the potential targets that ameliorate doxorubicin-induced cardiotoxicity (DIC), we aimed to investigate the role that macrophages play in the DIC development. Senescence of RAW264.7 cells was induced through doxorubicin administration in the experiment, and the transcription of secretory components was analyzed in this study.

overall_design: RAW264.7 cells were treated by medium and medium plus 100nM doxorubicin for 24h (n=5). [The concentration in the samples should be 100nM]

first: Wang

last: Heng

first: Xue

last: Song


title: The impact of Candida albicans on the transcriptome of Enterococcus faecalis when grown in a biofilm

city: Gainesville

first: Jessica

last: Kajfasz

address: 1395 Center Drive

department: Oral Biology

institute: University of Florida

summary: We sought to identify transcriptomic changes that arise when E. faecalis biofilms are cultivated in the presence of C. albicans. We used RNASeq analaysis to compare the transcriptome of 48 hr biofilm-grown cells of E. faecalis.  We compared the transcriptome of E. faecalis cells grown as a mono-species biofilm to that of E. faecalis cells that were grown in a biofilm that was co-inoculated with the yeast C. albicans.

overall_design: Cultures of E. faecalis OG1RF or C. albicans SC5314 were inoculated in BHI broth or Yeast Peptone Dextrose broth, respectively.  The cultures were grown to stationary phase, then cells were harvested by cetnrifugation and washed twice in sterile PBS.  The cell pellets were then suspended in BHI broth supplemented with 20mM glucose (BHIG).  The suspensions were adjusted to OD600 of 0.5 for E. faecalis (~3x10^9 CFU mL-1) or OD600 of 0.3 for C. albicans (~2.5x10^6 CFU mL-1).  Monospecies biofilms were initiated by adding 5mL of the E. faecalis suspension, while dualspecies biofilms were initiated by adding 2.5mL each of the E. faecalis and C. albicans suspensions to the wells of a 6-well plate.  The plates were incubated at 37C for 48hr in a 5% CO2 atmosphere, with fresh medium provided after 24 hrs.  After a total of 48hrs incubation, the media was removed and the cells of each well were suspended in 1mL of RNA Protect Bacterial Reagent (Qiagen).  Total RNA was isolated and prepared for RNA-Seq analysis.

first: Nicole

last: de Mello Fiallos

first: Jose

middle: A

last: Lemos


title: Harnessing STING Signaling and Natural Killer Cells to overcome PARP Inhibitor Resistance in Homologous Recombination Repair altered Breast Cancer


title: BMI-Associated Gene Expression Profiles in Adipose Tissue of Japanese Individuals

city: Tokyo

first: Naoki

last: Kobayashi

address: 1-21-1 Toyama, Shinjuku

department: Dept. of Molecular Diabetic Medicine

institute: National Center for Global Health and Medicine

summary: This dataset contains gene expression profiles from adipose tissue samples collected from Japanese individuals with varying body mass index (BMI). The study aims to investigate the association between BMI and gene expression patterns in adipose tissue, providing insights into the molecular mechanisms underlying obesity-related metabolic alterations. RNA was extracted from adipose tissue samples and analyzed using microarray technology. Differentially expressed genes associated with BMI were identified and may serve as potential biomarkers or therapeutic targets for obesity-related diseases.

overall_design: To identify candidate adipokines with gene expression alterations associated with obesity, a comprehensive gene expression analysis on human adipose tissue were conducted. The study included 176 subjects who were undergoing surgery for gastric cancer.

first: N

first: K

last: Hara

last: Ueki


title: Regulatory and structural variants in the CLCN2 gene are associated with modified skin colour pattern phenotypes in the corn snake.

city: Geneva

first: Athanasia

last: Tzika

address: Quai Ernest-Ansermet

department: Genetics and Evolution

country: Switzerland

institute: University of Geneva

summary: Background: Snakes exhibit a broad variety of adaptive colours and colour patterns, generated by the spatial arrangement of chromatophores, but little is known of the mechanisms responsible for these spectacular traits. Here, we investigate a monolocus trait with two recessive alleles that cause pattern aberrations in the corn snake: the motley and striped alleles. Results: We use mapping-by-sequencing to identify the genomic interval where the causal mutations reside. With our differential gene expression analyses, we find that CLCN2 (Chloride Voltage-Gated Channel 2), a gene within the genomic interval, is significantly downregulated in Motley embryonic skin. Furthermore, the insertion of a retrotransposon in CLCN2 results in a disruptive mutation in Stripe. We confirm the involvement of CLCN2 in colour pattern formation by producing knock-out snakes that present a phenotype similar to the Stripe one. In humans and mice, the disruption of CLCN2 results in leukoencephalopathy, as well as retinal and testes degeneration. Our single-cell transcriptomic analyses reveal that CLCN2 is indeed expressed in chromatophores during embryogenesis and in the adult brain. Although, we observe signs of vacuolation in the Stripe adult brain, the retina of Motley and Stripe animals is intact, and no fertility issues are reported for the carriers of both alleles. Conclusions: Our genomic, transcriptomic and functional analyses identify a plasma membrane anion channel to be involved in colour pattern development in Squamate reptiles and show that an active LTR-retrotransposon might be a key driver of trait diversification in corn snakes.

overall_design: To identify differentially expressed genes in the Motley morph of the corn snake, we sequenced dorsal skin samples from Motley and WT individuals at stage 7 (embryonic day 20)

first: Sophie

last: Montandon

first: Suzanne

middle: V

last: Saenko

first: Pierre

last: Beaudier

first: Asier

last: Ullate-Agote

first: Pierre-Yves

last: Helleboid

first: Maya

last: Kummrow

first: Sergi

last: Roig-Puiggros

first: Denis

last: Jabaudon

first: Leif

last: Andersson

first: Michel

middle: C

last: Milinkovitch


title: Harnessing STING Signaling and Natural Killer Cells to overcome PARP Inhibitor Resistance in Homologous Recombination Repair altered Breast Cancer [exome-Seq]

first: Lara

last: Nonell

overall_design: We leveraged Whole Exome Sequencing (WES) to analyse genomic alterations in PARPi-sensitive (MDA594) and PARPi-resistant (MDA594OR1 and MDA594OR2) tumor, in order to identify the mechanism of resistance to the PARPi olaparib.

first: Flaminia

last: Pedretti

first: Violeta

last: Serra


title: Regulatory and structural variants in the CLCN2 gene are associated with modified skin colour pattern phenotypes in the corn snake

overall_design: We performed single-nuclei RNAseq on brain and spinal cord from an adult Stripe corn snake using the 10x Genomics Chromium 3'GeneExpression kit. The cDNA libraries were quality controlled using a 2100 Bioanalyzer and TapeStation from Agilent and sequenced using a HiSeq 2500 sequencer from the iGE3 platform at the University of Geneva