title: SenPred: A single-cell RNA sequencing-based machine learning pipeline to classify deeply senescent dermal fibroblast cells for the detection of an in vivo senescent cell burden

city: London

first: Beth

last: Hughes

address: Blizard Institute, 4 Newark Street, Whitechapel

country: United Kingdom

institute: Queen Mary University London

summary:
Background - Senescence classification is an acknowledged challenge within the field, as markers are cell-type and context dependent. Currently, multiple morphological and immunofluorescence markers are required. However, emerging scRNA-seq datasets have enabled increased understanding of senescent cell heterogeneity.
Methods - Here we present SenPred, a machine-learning pipeline which identifies fibroblast senescence based on single-cell transcriptomics from fibroblasts grown in 2D and 3D.
Results - Using scRNA-seq of both 2D and 3D deeply senescent fibroblasts, the model predicts intra-experimental fibroblast senescence to a high degree of accuracy (>99% true positives). Applying SenPred to in vivo whole skin scRNA-seq datasets reveals that cells grown in 2D cannot accurately detect fibroblast senescence in vivo. Importantly, utilising scRNA-seq from 3D deeply senescent fibroblasts refines our ML model leading to improved detection of senescent cells in vivo. This is context specific, with the SenPred pipeline proving effective when detecting senescent human dermal fibroblasts in vivo, but not senescence of lung fibroblasts or whole skin.
Conclusions - We position this as a proof-of-concept study based on currently available scRNA-seq datasets, with the intention to build a holistic model to detect multiple senescent triggers using future emerging datasets.  The development of SenPred has allowed for detection of an in vivo senescent fibroblast burden in human skin, which could have broader implications for the treatment of age-related morbidities.

overall_design:
10x 3' scRNA-seq of primary human dermal fibroblasts isolated from facelift skin of a 42-year-old donor. Cells were grown in 2D in 6-well culture plates, or in 3D in a matrigel/collagen 1 dermal matrix.

Sample Type - DS2D, Barcode Suffix -1
Sample Type - DS3D, Barcode Suffix -2
Sample Type - EP2D, Barcode Suffix -3
Sample Type - EP3D, Barcode Suffix -4

first: Andrew

last: Davis

first: Deborah

last: Milligan

first: Ryan

last: Wallis

first: Federica

last: Mossa

first: Michael

last: Philpott

first: Linda

middle: J

last: Wainwright

first: David

last: Gunn

first: Cleo

last: Bishop


title: scRNA of lichen planus

status: Public on Dec 14 2024

city: Ann Arbor

first: Poulami

last: Dey

address: 1301 Catherine St

country: USA

institute: Michigan Medicine

type: Expression profiling by high throughput sequencing

summary: An early and sustained clinical response was seen, with 83.3% of patients responsive at week 16. Our molecular data identified a unique, oligoclonal IFN-γ, CD8+, CXCL13+ cytotoxic T-cell population in LP skin and demonstrated a rapid decrease in IFN signature within 2 weeks of treatment, most prominently in the basal layer of the epidermis.

overall_design: We conducted scRNA for skin and pbmcs in LP patients and normal individuals

first: Johann

middle: E

last: Gudjonsson

first: Lam

middle: C

last: Tsoi

first: Mangold

last: Aaron


title: Development of Fit Epidermal Resident Memory T Cells Requires Antigen Encounter in the Skin.

status: Public on Dec 10 2024

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

summary: CD8+ tissue resident memory T cells (TRM) develop from effectors that are recruited into peripheral tissues by infection or inflammation where they persist and provide defense against subsequent challenges.  Long-term persistence of epidermal TRM requires autocrine TGFβ that is transactivated by integrins expressed on keratinocytes.  In response to inflammation, the availability of TGFβ transactivation is limited.  Antigen-experienced TRM that encountered antigen in the epidermis during their development are more fit and outcompete bystander TRM for TGFβ transactivation resulting in their enrichment in the epidermis.  Transcriptomic analysis of endogenous epidermal TRM revealed that antigen-experienced TRM were enriched for TRM signature genes while bystander TRM retained the transcriptome of an earlier developmental state.  Following antigen recall, antigen-experienced TRM displayed accelerated proliferation kinetics compared with bystanders that was determined by the TCR signal-strength during their differentiation the skin.  Finally, antigen experienced TRM expressed TGFβRIII, which increases avidity of the TGFβRI/II receptor complex.  Selective ablation of Tgfbr3 from antigen experienced TRM reduced their capacity to persist when TGFβ activation was limited thus rendering them phenotypically like bystander TRM.  In sum, antigen-driven TCR signaling in the epidermis during TRM differentiation represents a required final step in ontogeny resulting in a lowered requirement on TGFβ transactivation for persistence and increased proliferation during recall responses that together result in the enhanced fitness of antigen-experience epidermal TRM.

overall_design:
Cohorts of wildtype C57BL/6 mice were infected on the left flank with VV by skin scarification.  DNFB was applied to the right flank 5 days post infection to recruit into the skin circulating CD8 effectors expanded by infection.  Mice were then rested for 50+ days to allow for the formation of TRM. Cells were pooled from 10 mice, enriched by percoll gradient centrifugation and purified by double FACSorting based on expression of CD90 and CD8.
On August 15, 2025, the Series was reorganized in order to include tissue-specific samples.

first: Eric

middle: S

last: Weiss

first: Toshiro

last: Hirai

first: Haiyue

last: Li

last: Lui

first: Shannon

last: Baker

first: Ian

last: Magill

first: Jingyu

last: Fan

last: Masopust

first: Niroshana

last: Anandasabapathy

first: Harinder

last: Singh

last: Zemmour

first: Laura

last: MacKay

first: Daniel

middle: H

last: Kaplan


title: Early spatiotemporal evolution of the immune response elicited by adenovirus vector vaccination

status: Public on Dec 05 2024

first: Dan

last: Barouch

address: 3 Blackfan Cir

department: CVVR

institute: Beth Israel Deaconess Medical Center

summary: As the first responders to immunological challenges, the innate immune system has the potential to shape and regulate the ensuing adaptive immune response. Many clinical studies evaluating the role of various innate populations in initiating vaccine-elicited immunity have been largely relegated to blood. It is also largely unknown how the immune response to vaccination is initiating and evolving at the earliest time points post-vaccination. We sought to investigate the spatiotemporal evolution of the earliest immune responses to intramuscular adenovirus serotype 26 (Ad26) vector vaccination in blood and tissues. Using transcriptomic profiling, we show that Ad26 vector vaccination elicits broad transcriptomic changes as early as 1 hour post-vaccination across blood and tissues marked by IL-1, TNF-α, and IL-6 pro-inflammatory pathways. Immunologic data reveals an influx of Ly6C+ myeloid cells into muscle by 1 hour post-vaccination. A Ly6C+CD64+ population emerges in muscle and subsequently in the draining lymph node, suggesting that myeloid cells may be significant drivers of vaccine-elicited immune responses following intramuscular vaccination. Moreover, levels of IL-6, MIG, MIP-1α, and MIP-1β measured in serum at 6 hours post-vaccination positively correlated with the frequency of vaccine-elicited CD8+ T cell responses evaluated at 60 days post-vaccination. Taken together, our data suggests that the immune response to Ad26 vector vaccination commences by 1 hour across compartments and that events at as early as 6 hours post-vaccination can shape vaccine-elicited CD8+ T cell responses at memory time points.

overall_design: In this study, we evaluated the early spatiotemporal evolution of the immune response following Ad serotype 26 (Ad26) vector vaccination, focusing on the first 24 hours post-vaccination. We evaluated transcriptomic signatures, cytokine and chemokine profiles, and cellular responses at various time points beginning as early as 1 hour post-vaccination to elucidate the induction of the immunological cascade. These studies highlight that the immune response commences by 1 hour and rapidly evolves across blood and tissues within the first 24 hours post-vaccination.

first: Eryn

last: Blass

first: Malika

last: Aid

first: Zi

last: Kang

first: M

last: Iampietro

first: R

middle: K

last: Reeves

first: Alessandro

last: Colarusso


title: An increase in ROS is required for repair of the neonatal cerebellum

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The neonatal mouse cerebellum shows remarkable regenerative potential upon injury at birth. Nestin-expressing progenitors (NEPs) undergo adaptive reprogramming to replenish the lost granule cell progenitors. Here, we investigate how the injury microenvironment affects NEPs’ regenerative potential and adaptive reprogramming. Single cell transcriptomic and bulk chromatin accessibility analyses of the NEPs from control and injured neonatal cerebella show a temporary increase in mechanisms involved in the response to reactive oxygen species (ROS), a known damage-associated molecular pattern. Analysis of ROS levels also confirms a temporary increase in ROS levels upon injury at postanal day 1, 1-2 days after injury, overlapping with the induction in cell death in the cerebellum. Using a transgenic mouse model that overexpresses mitochondrial catalase (mCAT) and reduces ROS levels globally, we showed that the regenerative potential of NEPs decreases upon injury to the granule cell progenitors at birth and the repair is impaired. Finally, we demonstrated that microglia are involved in adaptive reprogramming by regulating NEP migration to the external granule layer, the site of injury. Collectively, our results highlight that the changes in the tissue microenvironment such as an increase in the ROS levels are required for the adaptative reprogramming of NEPs upon injury to the granule cell progenitors at birth, highlighting the instructive roles of microenvironmental signals during regeneration in the neonatal brain.

overall_design: Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) was used to profile control or irradiated nestin-expressing progenitors (NEPs) from the mouse cerebellum

first: Sumru

last: Bayin

middle: P

first: Alex

middle: L

last: Joyner


title: Bulk RNA-seq of primary keratinocytes treated with IgG from patients with bullous pemphigoid or controls I

status: Public on Dec 04 2024

city: Chicago

first: kyle

last: amber

state: IL

address: 707 S Wood St

institute: Rush University

summary: While antibodies in bullous pemphigoid (BP) are known to activate innate immune response, their direct effect on keratinocytes and the overall contribution of keratinocytes to disease pathogenesis is largely unknown. We sought to understand the mechanism of keratinocyte response to autoantibodies in BP.  We affinity purified IgG from patients with a known diagnosis of bullous pemphigoid or healthy controls, and performed bulk RNA-seq. We identified numerous differentially expressed genes including upregulation of CXCL16, IL-24, and TGFB1 in BP-IgG treated keratinocytes

overall_design: Primary human keratinocytes were treated with 4mg/mL of affinity purified IgG from patients with bullous pemphigoid (n=4) or control (n=4)

first: Amber

last: Kyle


title: Bulk RNA-seq of primary keratinocytes treated with IgG from patients with bullous pemphigoid or controls II

first: Kyle

last: Amber


title: Cell-type-specific RNA Pol II activity maps in intact-tissues: gateway to mammalian gene regulatory mechanisms in vivo [RNA-seq]

city: Ithaca

first: Tudorita

last: Tumbar

state: NY

address: 526 Campus Rd

department: Molecular biology and genetics

institute: Cornell University

summary: Accessing ongoing RNA Pol II activity in specific cell types within intact-tissue is critical to reveal regulatory mechanisms of development. We developed PReCIS-seq, a method combining Cre-inducible GFP-tagging of endogenous Pol II with transcriptional run-on and GFP-immunoprecipitation, to map transcriptionally-engaged Pol II genome-wide in targeted cell types of mouse tissues. Applied to keratinocytes within intact-skin, PReCIS-seq demonstrates that transcriptionally activated functions of biological transitions generally employ both Pol II promoter-recruitment and promoter-proximal pause-release mechanisms. We uncover a global Pol II regulatory polarization that modulates cellular safeguarding versus lineage identity genes across embryonic development to adult homeostasis. This polarization is associated with distinct proximal-promoter structures distinguishing high-paused genes with restricted Pol II pause-release from low-paused genes undergoing rapid Pol II firing into productive elongation. PReCIS-seq also identifies active enhancers based on divergent transcription. This approach enables high-resolution, cell-type-specific analysis of Pol II dynamics in intact-tissues across mammalian development, homeostasis, and disease.

overall_design: To check correlation of nascent RNA levels with steady-state RNA levels, we performed Bulk RNA sequencing of GFP+ telogen skin keratinocytes that were FACS sorted from the mouse skin tissue.

first: Gopal

last: Chovatiya


title: Cell-type-specific RNA Pol II activity maps in intact-tissues: gateway to mammalian gene regulatory mechanisms in vivo [ChIP-seq]

overall_design: Functional validation of cell-type-specific RPB2-GFP tagging using ChIP-seq. Conventional ChIP-seq on mouse skin tissue was performed on Cre negative and Cre positive mice carrying Polr2b.fl.fl.GFP allele using IgG, PolII (8WG16), and GFP antibodies.


title: Cell-type-specific RNA Pol II activity maps in intact-tissues: gateway to mammalian gene regulatory mechanisms in vivo [PReCIS_seq]

overall_design: Cell-type-specific nascent trascriptomics in vivo using PReCIS-seq was performed on skin keratinocytes at different stages of hair follicle cycle. Whole skin samples without GFP immunoprecipitation were used as input controls. For ex vivo samples, PRO-seq was performed on freshly isolated skin keratinocytes and cultured keratinocytes.


title: Multiomics profiling of hematopoietic differntiation from hPSCs and crod blood CD34+ cells

status: Public on Dec 02 2024

city: Madison

first: Igor

middle: I.

last: Slukvin

address: 1220 Capitol Court

institute: University of Wisconsin

summary: Single cell RNAseq and ATACseq was performed with cells isolated from day 4, day 5 and day 8 hPSC differntiation cultures and cordb lodd CD34+ cells.

overall_design: hPSC subjected to hematopoietic differntiation in serum-free and fedder free conditions. KDR+ and CD31+ cells isolated by FACS on day 4 or day 5 and 8, respectively and subjected to molecular profiling.

first: Ho Sun

last: Jung

first: Peng

last: Liu


title: Developmental programming of Kupffer cells by maternal obesity causes fatty liver disease in the offspring [snMultiome sequencing]

city: Bonn

first: Elvira

last: Mass

address: Carl-Troll-Str, 31

department: LIMES

country: Germany

institute: University of Bonn

summary: Kupffer cells (KCs) are tissue-resident macrophages which colonize the liver early during embryogenesis. KCs start to acquire a tissue-specific transcriptional signature immediately after colonizing the liver, mature together with the tissue, and adapt to the tissue’s functions. Throughout development and adulthood, KCs have distinct core functions that are essential for liver and organismal homeostasis, such as supporting fetal erythropoiesis as well as postnatal erythrocyte recycling and liver metabolism. However, whether perturbations of macrophage core functions during development contribute to or cause disease at postnatal stages is poorly understood. Here, we utilize a mouse model of maternal obesity to perturb KC functions during gestation. We show that offspring exposed to maternal obesity develop fatty liver disease, driven by aberrant developmental programming of KCs that persists into adulthood. Programmed KCs mediate lipid uptake by hepatocytes through apolipoprotein secretion. KC depletion in neonates born to obese mothers, followed by replenishment with exogenous monocytes, rescues the fatty liver disease. The transcriptional programming of KCs and the fatty liver disease phenotype are also rescued by genetic depletion of hypoxia-inducible factor alpha (Hif1a) in macrophages during gestation. These results establish developmental perturbation of KC functions as a cause for the development of fatty liver disease in adult life and, thereby, place fetal-derived macrophages as intergenerational messengers within the concept of developmental origins of health and diseases.

overall_design: Three-week-old female mice were initially fed with a control diet (CD) for two weeks and were thereafter divided into two groups: one continued on the CD while the other received a high-fat diet (HFD) for eight weeks. The homeostatic model for insulin resistance (HOMA-IR) was used to assess metabolic changes. Mice with higher HOMA-IR on the HFD were selected to create a maternal obesity model and mice fed with CD were used to generated maternal lean offspring. All females were mated with CD males. Offspring born to maternal obese were cross-fostered to generate both lactating groups and offspring born to maternal lean mothers were crossed-fostered by other maternal lean mothers. Male offspring were weaned into CD or HFD postweaning cages. Livers of offspring were harvested at 11-12 weeks. Nuclei were isolated from approximately 50 mg of flash-frozen adult liver tissue to enable simultaneous single-nucleus RNA sequencing (snRNA-seq) and single-nucleus ATAC sequencing (snATAC-seq), capturing both transcriptional profiles and chromatin accessibility.

first: Hao

last: Hunag

first: Nelli

last: Blank-Stein

first: Lea

last: Seep


title: A pancreas–hippocampus feedback mechanism regulates circadian changes in depression-related behaviors

status: Public on Dec 01 2024

city: beijing

first: xinyu

last: She

address: shuangqing road, haidian district

department: school of life sciences

country: China

institute: Tsinghua university

summary: Individuals with neuropsychiatric disorders often show metabolic symptoms. However, the mechanisms underlying this co-occurrence remain unclear. Here, we show that iPSC-derived pancreatic islets from individuals with bipolar disorder (BD) have insulin secretion deficits caused by increased expression of RORβ, a susceptibility gene for BD. Enhancing RORβ expression in mouse pancreatic β-cells induced depression-related behaviors in the light phase and mania-like behaviors in the dark phase. Pancreatic RORβ overexpression in the light phase reduced insulin release from islets, inducing hippocampal hyperactivity and depression-like behaviors. Further, this hippocampal hyperactivity in the light phase had the delayed effect of promoting insulin release in the dark phase, resulting mania-like behaviors and hippocampal neuronal hypoactivity. Our results in mice point to a pancreas–hippocampus feedback mechanism by which metabolic and circadian factors cooperate to generate behavioral fluctuations and which may play a role in bipolar disorder.

overall_design: The experimental conditions and variables under investigation included replicates. We utilized neurons and islet-like organoids derived from healthy controls who had no psychiatric disorders, serving as the control group.

first: Yao-Nan

first: Qiu-Wen

last: Wang

first: Xin-Yu

first: Li-Jun

last: Li

first: Bing

first: Rui-Lan

last: Yang

first: Qian

first: Si-Yao

last: Lu

first: Ying-Han

first: Wei

last: Shen

first: Chong-Lei

last: Fu

first: Lan

last: Yi

first: Chun-Xue

last: Shi

first: Xin

last: Cheng

first: Li-Ping

last: Cao

first: Shuang-Li

last: Mi

first: Dan

first: Jun

last: Yao


title: Aberrant pace of cortical neuron development in brain organoids from patients with 22q11.2 deletion syndrome and schizophrenia. [miRNA-Seq]

first: Bin

last: Xu

address: 1051 Riverside Dr

department: Psychiatry

institute: Columbia University

type: Non-coding RNA profiling by high throughput sequencing

summary: Adults and children with the 22q11.2 deletion syndrome (22q11.2DS) demonstrate cognitive, social and emotional impairments and markedly increased risk for schizophrenia (SCZ). The alterations in early human brain development resulting from this deletion remain unclear. Here we use organoid models of the developing human cerebral cortex derived from patients with 22q11.2DS and SCZ as well as unaffected controls to identify cell-type-specific developmental abnormalities that result from this genomic lesion. Using RNA-sequencing and follow-up experimental validation we find that loss of genes within the 22q11.2 locus leads to delayed development of cortical neurons.

overall_design: We perfomed miRNA expression profiling from organoid models of the developing human cerebral cortex. The organoids were derived from 3 hiPSC lines from patients with 22q11.2DS and SCZ as well as 3 unaffected controls matched by sex and age.

first: Sneha

last: Rao

first: Joseph

last: Gogos


title: Effect of depletion of Pcyt2 on gene expression in the early myotome.

city: Vienna

first: Maria

last: Novatchkova

address: Dr Bohrgasse

country: Austria

institute: IMP/IMBA

summary:
To investigate the cosequence of Pcyt2 deletion in the early myotome, we established Myf5Cre-Pcyt2 mouse line in which each target gene has been depleted in the early developing myotome and onwards in the mature muscle.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells at two time points.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for developing muscle in  control (Pcyt2 flox/flox) mice and Myf5Cre-Pcyt2 experimental group on the same background with muslces defficient for Pcyt2..

first: Cikes

last: Domagoj


title: Aberrant pace of cortical neuron development in brain organoids from patients with 22q11.2 deletion syndrome and schizophrenia.

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

overall_design: Refer to individual Series


title: SMAC mimetics induce human macrophages to phagocytose live cancer cells

status: Public on Nov 30 2024

city: Brookline

first: Li

last: Qiang

address: 1 Jimmy Fund Way

institute: Dana-Farber Cancer Institute

summary: Macrophages engulf apoptotic bodies and cellular debris as part of homeostasis, but they can also phagocytosis live cells such as aged red blood cells. Pharmacologic reprogramming with the SMAC mimetic LCL-161 in combination with T cell-derived cytokines can induce macrophages to phagocytosis live cancer cells in mouse models. Here we extend these findings to encompass a wide range of monovalent and bivalent SMAC mimetic compounds, demonstrating that live cell phagocytosis is a class effect of these agents. We demonstrate robust phagocytosis of live pancreatic and breast cancer cells by primary human macrophages across a range of healthy donors. Unlike mouse macrophages where combination of SMAC mimetics with lymphotoxin enhanced phagocytosis, human macrophages were more efficiently polarized to phagocytose live cells by the combination of SMAC mimetics and IFNg. We profiled phagocytic macrophages by transcriptional and proteomic methodologies, uncovering a positive feedback loop of autocrine TNFa production.

overall_design: PBMCs were isolated from eight individual donors and differentiated into macrophages. For each donor, macrophages were treated for 24 hours with either DMSO, rhLTα1/β2, IFN-γ, LCL-161 (500nM), LCL-161 + rhLTα1/β2, or LCL-161 + IFN-γ. After treatment, macrophages were harvested, and total RNA was extracted using the RNeasy Mini Kit (Qiagen, Cat# 74104) according to the manufacturer’s protocol. (company). Additionally, phagocytosis assays were performed on treated macrophages from all donors to ensure treatment response.

first: Samantha

last: Liu

first: Max

last: Hulsman

first: Philipp

last: Leyendecker

first: Eugena

last: Chang

first: Katherine

last: Donovan

first: Fabian

last: Strobel

first: James

last: Dougan

first: Fisher

last: Eric

first: Michael

first: Stephanie


title: A multitargeting approach rewires cell identity in fusion-negative rhabdomyosarcoma [snRNAseq and scATACseq]

status: Public on Nov 27 2024

city: Leuven

first: Maurilio

last: Sampaolesi

address: Herestraat 49, ON4 - box 804

department: Department of Development and Regeneration

country: Belgium

institute: KU Leuven

summary: Rhabdomyosarcoma (RMS), the most common soft-tissue sarcoma occurring in the pediatric population, arises from the skeletal muscle compartment. Several transcriptional and post-transcriptional regulators lock the tumor in a continuous undifferentiated state and prevent the cells from returning to quiescence. MicroRNAs (miRNAs) are short non-coding RNAs that modulate cell identity by means of post-transcriptional regulation of messenger RNAs. In this study, we aimed at identifying miRNAs that could affect FN-RMS cell identity. Thus, we analyzed publicly available datasets and identified miR-449a and miR-340 as the main regulators of cell cycle and p53 signaling. Using miR-eCLIP technology, we identified the direct effects of miRNAs in FN-RMS cell lines, and an overall rewiring of cell identity at the transcriptomic, epigenetic and metabolic level. We observed that miR-449a+340 directly and indirectly targeted glycolysis and pyruvate entry into mitochondria by inhibiting mitochondrial pyruvate complex (MPC) inhibition. The pharmacological inhibition of MPC resulted in a similar metabolic shift with cell cycle exit and a significant reduction in metastatic potential of FN-RMS models. In conclusion, the combination of miR-449 and miR-340 play a pivotal role in orchestrating the cell identity of FN-RMS, and the modulation of MPC emerges as a key factor in redirecting FN-RMS towards a quiescent, non-tumorigenic state.

overall_design: Human fusion-negative rhabdomyosarcoma (FN-RMS) cell line RD18 was transfected with either lipofectamine or miR-449a + miR-340 for 60 hours, and subsequently single-nuclei multiomic RNAseq and ATACseq was performed

first: Enrico

last: Pozzo


title: Clonorchis sinensis (C. sinensis) infection remodels the chromatin accessibility of hepatocellular carcinoma

status: Public on Nov 26 2024

city: Nanning

first: Min

last: Fang

state: None Selected

address: Guangxi Medical University Cancer Hospital 71, Hedi Road, Qingxiu District

department: Department of Clinical Laboratory

summary: Background: Liver cancer is the third deadliest type of cancer, posing a serious threat to human health. Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer. C. sinensis, classified as a definite group I carcinogen by the IARC (International Agency for Research on Cancer), is an important risk factor for HCC. Although many studies have shown that C. sinensis infection affects the prognosis of HCC patients, the specific mechanisms are still unclear, especially the dynamics and regulatory roles of chromatin accessibility. Results: In this study, we integrated ATAC-seq, RNA-seq, and ChIP-seq data to elucidate changes in the epigenetics of HCC after the C. sinensis infection. Many different accessibility regions (DARs) were identified both in tumors and adjacent tissue after the C. sinensis infection. Meanwhile, top TFs whose motifs were enriched in DAR were found, such as HNF4a, FOXI1, etc. Although there were slight deviations, epigenetic changes were found to be consistent with gene expression levels. We also revealed that H3K9ac, H3K4me2, H3K4me3, H3K27ac, and H3K4me1 were associated with chromatin accessibility. Importantly, we also found potential evidence that C. sinensis infection would alter the spatial structure of the HCC genome. Finally, both molecular experimental results and clinical data certified that C. sinensis infection would promote the metastasis of HCC. Conclusions: C. sinensis infection will remodel the chromatin accessibility of HCC, leading to changes in gene expression levels. This study provides conclusive evidence that C. sinensis infection alters the epigenetics of HCC.

overall_design: Comparatine gene expression profling analysis of ATAC‑seq data and RNA-seg data for Cs+ and Cs－ HCC

first: Weilong

last: Yang

first: Caibiao

last: Wei

first: Junxian

last: Chen


title: STING inhibition alleviates experimental peritoneal damage: potential therapeutic relevance for peritoneal dialysis

status: Public on Nov 25 2024

city: Madrid

first: Vanessa

last: Marchant

state: Madrid

address: Avda. Reyes Católicos, 2

department: IIS-FJD

country: Spain

institute: Universidad Autónoma de Madrid

summary: Peritoneal dialysis (PD) is a widely used kidney replacement therapy for patients with end-stage kidney disease. Nevertheless, long-term exposure to PD fluid can damage the peritoneal membrane, leading to ultrafiltration failure and, ultimately, discontinuation of PD. Investigation of the molecular mechanisms underlying this damage is essential for identifying new therapeutic targets to mitigate peritoneal deterioration in PD patients. To this end, we employed RNA sequencing in a preclinical model of peritoneal injury, induced by prolonged chlorhexidine (CHX) exposure, which revealed cytosolic DNA-sensing signaling as a novel pathway. Next, we demonstrated that key players in this pathway, such as the stimulator of interferon genes (STING) and its downstream signaling effectors (interferon regulatory factor 3, interferon-stimulated genes, and nuclear factor-κB signaling), were upregulated in experimental peritoneal damage. Moreover, increased STING expression was observed in human peritoneal biopsies from patients with PD. Subsequent studies in STING-deficient mice showed reduced proinflammatory gene expression and immune cell infiltration, together with inhibited nuclear factor-κB pathway activation at both early (10 days) and late (30 days) stages of CHX-induced peritoneal injury. STING deficiency also reduced peritoneal membrane thickening, fibrosis, and mesothelial-to-mesenchymal transition (MMT)-related changes in advanced CHX-induced damage. Furthermore, pharmacological inhibition of STING with C-176 attenuated CHX-induced peritoneal inflammation. Macrophages were identified as one of the STING-expressing cell types in the injured peritoneum. Hence, in vitro STING blockade in activated macrophages inhibited MMT in cultured mesothelial cells, suggesting that STING activation in this population may drive peritoneal fibrosis. Additionally, STING deficiency reduced peritoneal inflammation in S. epidermidis-induced peritonitis and decreased adhesion scores in a postsurgical intra-abdominal adhesion model. These findings identify STING as a pivotal mediator of peritoneal injury and support its potential as a novel therapeutic target to prevent PD-associated ultrafiltration failure. © 2025 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

overall_design:
To profile the transcriptomic changes during the peritoneal injury in order to identify new mediators of damage, we performed a RNA-seq study in peritoneal tissue from mice of a chlorhexidine gluconate (CHX)-induced damage model. Mice were intraperitoneally injected with 0.1% CHX in saline solution daily for 10 consecutive days (n = 4, CHX group). Untreated mice were used as control group (n = 4). After treatment, mice were euthanized and parietal peritoneum samples were collected  and frozen in liquid nitrogen until processing.
The gene expression profiling analysis was perfomed using the data of RNA-seq of two group of mice (Control and CHX), with 4 mice per group.
Differential expression analysis was carried out comparing data from CHX group versus Control group

first: Marta

last: Ruiz-Ortega

first: Adrián

middle: M

last: Ramos


title: Single-cell RNA Sequencing Uncovers Molecular Mechanisms of Human Pancreatic Islet Dysfunction Under Overnutrition Metabolic Stress

status: Public on Nov 20 2024

city: Tallahassee

first: Li

last: Guo

address: Thrasher Medical Researcher Building, Suite 2300-D

department: College of Medicine

institute: Florida State University

summary: Metabolic stress elicits functional changes in pancreatic islets, contributing to the pathogenesis of type 2 diabetes. However, the molecular mechanisms underlying overnutrition stress in islet cells is not well understood. In our study, we subjected human islets to overnutrition with 25 mM glucose and 0.5 mM palmitic acid or a control culture condition with 5.1 mM glucose. We utilized single-cell RNA sequencing to comprehensively characterize the gene expression changes between these two conditions in a cell-type specific manner. We found that among all islet endocrine cell types, alpha cells are the most resilient to glucolipotoxicity, while beta cells are the most susceptible. Additionally, we observed a reduction in cell-cell interactions within islet endocrine cells under glucolipotoxic conditions, alongside alterations in gene regulatory networks linked to type 2 diabetes genetic risk. Lastly, targeted drug screening underscored the critical role of histone H3K9 methyltransferases G9a and GLP in modulating the cellular response to overnutrition.

overall_design: Human islets were cultured for 48 hours under either 5.1mM glucose (control) or 25mM glucose + 0.5mM palmitic acid (glucolipotoxicity condition). Islets from three male and three female control donors were dissociated and processed for single-cell RNA sequencing.

first: Yue

last: Wang


title: CHIP-seq for NKX2-3 overexpressing tumor pericytes

city: Guang Zhou

first: Qun

last: Miao

address: Huangpu avenue

institute: Jinan University

summary: This study aims to investigate genes regulated by NKX2-3

overall_design: The tumor pericytes were infected with lentiviruses carrying vector or NKX2-3 overexpression plasmids. Essentially, cells were crosslinked with formaldehyde. After chromatin sonification and centrifugation, 2% of the digested chromatin was saved and the remaining chromatin was equally divided into two aliquots, one for immunoprecipitation by anti-NKX2-3 antibody (HPA047561, Sigma, Shanghai, China), and other as the negative control by adding anti-IgG. After elution from antibody/protein G magnetic beads and reversing the cross-links, the immunoprecipitated DNA was purified and purified for sequencing.

first: Dongmei

last: Zhang

first: Minfeng

first: Sishan

last: Yan

first: Xiaobo

last: Li


title: Single-cell atlases of Aedes aegypti midgut and fat body reveal cellular and metabolic dynamics after a blood-meal

status: Public on Nov 17 2024

city: Paris

first: Thomas

last: Vial

address: 28 rue du Docteur Roux

country: France

institute: Institut Pasteur

summary: Aedes aegypti mosquito, vector for several viral diseases, undergoes significant physiological changes after a blood meal. Through single-cell RNA sequencing and metabolomics, we unveiled dynamic cellular composition and metabolic adaptations within abdominal midgut and fat body tissues. We revealed high cell diversity, specialized in digestion, metabolism, immunity, and reproduction. While the midgut primarily comprises enterocytes, enteroendocrine, cardia and intestinal stem cells, the fat body consists of not only trophocytes and oenocytes, but also a substantial population of hemocytes and fat body-yolk cells (FYC). The fat body, exhibiting a more complex metabolomic profile than the midgut, played a central role in immune and metabolic gene expression, particularly within trophocytes and FYCs. Additionally, insect-specific viruses were detected at the single-cell level, mainly in the midgut at later stages post-blood meal. These findings offer new vector control strategies by targeting specific abdominal cell populations and metabolic pathways involved after a blood meal.

overall_design: Midgut and fat body cells were isolated from Aedes aegypti mosquitoes at 2 and 7 days post-blood meal. For each time point, seven midguts and seven fat bodies were subjected to a cold dissociation method, generating two independent single-cell suspensions for scRNAseq analyses. The cells were then processed for single-cell RNA sequencing using the 10X Chromium Next GEM Single Cell 5' Kit v2 dual index. Libraries were sequenced by Macrogen on a NovaSeq 6000 platform (Illumina).

first: Hélène

last: Lopez-Maestre

first: Sarah

last: Merkling


title: Aberrant pace of cortical neuron development in brain organoids from patients with 22q11.2 deletion syndrome and schizophrenia. [bulk RNA-Seq]

first: Bin

last: Xu

overall_design: We perfomed gene expression profiling from organoid models of the developing human cerebral cortex. The organoids were derived from 4 hiPSC lines from patients with 22q11.2DS and SCZ as well as 4 unaffected controls matched by sex and age.

first: Sneha

last: Rao

first: Joseph

last: Gogos


title: Expression Analysis between HUVECs and EndMTed HUVECs

status: Public on Nov 28 2024

city: Tsu

first: Takumi

last: Kageyama

state: Mie

address: 2-174 Edobashi

department: Department of Nephro-Urologic Surgery and Andrology

country: Japan

institute: Mie University Graduate School of Medicine

summary: Prostate cancer often progresses to castration-resistant prostate cancer (CRPC), with neuroendocrine prostate cancer (NEPC) representing a highly aggressive variant. This study shows that endothelial-to-mesenchymal transition (EndMT) in vascular endothelial cells, induced by IL-1β and TGF-β2, enhances neuroendocrine differentiation in prostate cancer cells. LNCaP cells co-cultured with EndMTed HUVECs exhibited increased expression of neuroendocrine markers such as chromogranin A. GM-CSF emerged as a key mediator in this process, and its addition under androgen deprivation conditions further elevated neuroendocrine marker expression. Anti-androgen therapy with enzalutamide also paradoxically increased IL-1β and TGF-β2 secretion, promoting EndMT and subsequent neuroendocrine differentiation. These results highlight the potential of targeting EndMT and GM-CSF pathways as therapeutic strategies for aggressive, treatment-resistant forms of NEPC.

overall_design: To investigate the factors excreted by EndMTed HUVECs, which might induce neuroendocrine differentiation of LNCaP cells, we performed a comprehensive expression analysis to compare differences in expression between HUVECs and EndMTed HUVECs by RNA-Seq.

first: Sho

last: Sekito

first: Yasuhiro

last: Murakawa

first: Takahiro

last: Inoue


title: Transcriptomic changes in ER-HOXB8 mouse cell line on Phf6 knockout

status: Public on Nov 15 2024

city: Philadelphia

first: Vikram

middle: R

last: Paralkar

state: PA

address: 421 Curie Boulevard

department: Division of Hematology and Oncology, Department of Medicine

institute: University of Pennsylvania Perelman School of Medicine

summary: PHF6 is a transcriptional regulator mutated in 3-5% of acute myeloid leukemia. To understand the effect of loss and clinical mutation of PHF6 on the transcriptome of myeloid cells we generated multiple wildtype and Phf6 knockout clones. We observed that loss of PHF6 upregulated genes related to stemness and downregulates genes related to myeloid differentiation.

overall_design: RNA-Seq of wildtype and Phf6 knockout ER-HOXB8 mouse GMP cells that were clonally selected and expanded after Cas9-gRNA lentiviral transduction.

first: Aishwarya

last: Pawar

first: Subin

last: George


title: PHIP occupancy in THP1 human AML cell line

summary: PHF6 is a transcriptional regulator mutated in 3-5% of acute myeloid leukemia. To understand how PHF6 and its functional partner PHIP interact with each other on chromatin, we performed ChIP-Seq for PHF6 (in the presence and absence of PHIP), for PHF6R274Q mutant, and for PHIP. We observd that PHF6 and PHIP peaks overlap on chromatin, and PHF6 requires PHIP for its chromatin occupancy. ATAC-Seq and H3K27ac ChIP-Seq showed that PHF6 and PHIP occupy open and active regions of the genome.

overall_design: PHIP ChIP-Seq in wildtype THP1 AML cells


title: PHF6 occupancy in THP1 human AML cell line in wildtype, PHF6R274Q mutant, and PHIP knockout cells

overall_design: PHF6 ChIP-Seq in PHF6 wildtype, PHF6R274Q mutant, and PHIP knockout THP1 AML cells that were clonally selected and expanded after Cas9/RNP and sgRNA transfection.


title: Transcriptome comparison of RhoP23H/+ mouse retina with wildtype at different age

city: Pittsburgh

first: Yuanyuan

last: Chen

address: 1622 Locust Street,

department: Ophthalmology

institute: University of Pittsburgh

summary: Rhodopsin P23H mutation is the most comment mutation causing autosomal dominant retinitis pigmentosa in the USA. The goal of this project is to compare the transcriptome changes of the Rhodopsin P23H knock-in mouse model of adRP to the wildtype control at different ages. The transcriptomic profile will help us understand the molecular events along the pathophysiology of reititis pigmentosa in this mouse model. We include the RNA seq data of Rhodopsin P23H heterozygous mouse retinas at 1, 3 and 6 months of age to compare with age-matched wildtype mouse retinas. N=3 and each sample is from an individual animal.

overall_design: Heterozygous Rhodopsin P23H knock-in mice (B6.129S6(Cg)-Rhotm1.1Kpal/J) and wildtype mice were euthanized at 1, 3 and 6 months of age and their retinas were isolated fresh. Total RNA was isolated using the Tryzol kit and RNA integrity was checked by Agilent Bioanalyzer. Libraries for RNA-Seq were prepared with KAPA Stranded mRNA-Seq poly(A) selected kit (KAPA Biosystems, Wilmington, MA)using 250 ng total RNAs for each sample. Quality checks with a bioanalyzer were also performed on each library. Paired end sequencing was performed on Illumina HighSeq 4000 (Illumnia Inc., San Diego, CA).  The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 [1]and the gene expression level was estimated using RSEM v1.2.15.[2] TMM (trimmed mean of M-values) was used to normalize the gene expression. Differentially expressed genes were identified using the edgeR program[3]. Genes showing altered expression with p < 0.05 and more than 1.5 fold changes were considered differentially expressed. Goseq was uesd to perform the GO enrichment analysis and Kobas was used to performed the pathway analysis.


title: Chromatin accessibility changes caused by PHF6 knockout in THP1 human AML cell line

summary: PHF6 is a transcriptional regulator mutated in 3-5% of acute myeloid leukemia. To understand how PHF6 and its functional partner PHIP interact with each other on chromatin, we performed ChIP-Seq for PHF6 (in the presence and absence of PHIP), and for PHIP. We observd that PHF6 and PHIP peaks overlap on chromatin, and PHF6 requires PHIP for its chromatin occupancy. ATAC-Seq and H3K27ac ChIP-Seq showed that PHF6 and PHIP occupy open and active regions of the genome.

overall_design: ATAC-Seq of wildtype and PHF6 knockout clones in human THP1 cell line


title: Transcriptomic changes in PHF6 knockout THP1 human AML cell line on rescue with PHF6 wildtype (with and without PHIP) or rescue with PHF6R274Q mutant

summary: PHF6 is a transcriptional regulator mutated in 3-5% of acute myeloid leukemia. To understand the effect of loss and clinical mutation of PHF6 on the transcriptome of myeloid cells, we generated multiple wildtype and PHF6 knockout clones, as well as clones expressing the most common clinical mutant of the protein-PHF6R274Q. We observed that both single and double knockouts and mutation of PHF6 shifted the cells towards stemness and away from differentiation. Additionally we identified PHIP as a possible functional partner for PHF6. To investigate their common biological function, we generated multiple single knockout clones of PHIP as well as double knockout clones of PHIP and PHF6, and observed that, similar to single knockout of PHF6, PHIP knockout and double knockout also shifted cells towards stemness and away from differentiation. Collectively, our experiments show that PHF6 and PHIP, separately identified as being mutated in AML, exert similar downstream effects on the AML transcriptome.

overall_design: RNA-Seq of wildtype PHF6 rescue, in presence and absence of PHIP, and rescue of PHF6R274Q mutant in a null background


title: Changes in H3K27 acetylation in THP1 human AML cell line on PHF6 knockout, PHF6R274Q mutation, PHIP knockout, and double knockout of PHF6 and PHIP compared to wildtype clones

overall_design: H3K27ac ChIP-Seq of wildtype, PHF6 knockout, PHF6R274Q mutant, PHIP knockout, and PHF6/PHF6 double-knockout in THP1 AML cells that were clonally selected and expanded after Cas9/RNP and sgRNA transfection


title: Timing of Ezh2Y641F mutation determines oncogenic and molecular outcomes in hematologic diseases

status: Public on Nov 14 2024

city: St. Louis

first: George

middle: P.

last: Souroullas

state: Missouri

address: 660 S. Euclid Ave

department: Department of Medicine

institute: Washington University School of Medicine

summary: Enhancer of Zeste Homolog 2 (EZH2) functions as the catalytic component of the Polycomb Repressive Complex 2, a chromatin modifying complex, which mediates methylation of lysine 27 on histone 3 (H3K27me3), a repressive chromatin mark.  In cancer, genetic alterations in EZH2 encompass amplifications, deletions and point mutations, and of particular interest are the recurring mutations in the SET domain at tyrosine 641 (Y641).  Hematologic malignancies exhibit a prominent association with EZH2Y641 mutations, primarily observed in B cell malignancies such as germinal center diffuse large B cell lymphoma (DLBCL) and follicular lymphoma (FL) with a mutation frequency around 20%.  Leukemias and solid tumors like melanoma, prostate, head and neck, sarcomas, and others demonstrate substantially lower EZH2Y641 mutation frequencies.  Because the effect of Ezh2Y641F mutations depend on the existing patterns of H3K27 mono-, di-, and tri-methylation, we hypothesized that the oncogenic potential of Ezh2Y641F mutations depends on the developmental stage and cell of origin during which mutations occur.  Towards that end, we employed a conditional and inducible mouse model of Ezh2Y641F, crossed with different tissue-specific Cre drivers. We found that heterozygous expression of Ezh2Y641F early in embryonic development, at birth, or in adult hematopoietic stem/progenitor cells resulted in diminished overall survival, which was primarily attributed to hematopoietic defects.  Specifically, expression of Ezh2Y641F at the hematopoietic stem cell (HSC) stage did not induce B cell or myeloid transformation, but instead led to bone marrow failure due to both cell intrinsic and cell extrinsic factors.   Analysis of gene expression profiles in pro- and pre pro-B cells isolated from the CD19-Cre and Mx1-Cre crosses demonstrated a significant overlap in differentially expressed genes and pathways such as IFN signaling and IL2-Stat5 signaling.  Expression of Ezh2Y641F at different times during hematopoietic development also resulted in expression of different pathways in early B cell progenitors, such as E2F targets, heme metabolism and GTPase activity driven by GBP proteins.  Forced expression of Gbp2/3 in several lymphoma/leukemia cell lines revealed subtle changes in cell survival, suggesting a possible mechanism for how expression of Ezh2Y641F could have a different effect on hematopoietic transformation depending on when it is expressed.  In summary, our study underscores the critical importance of the timing of the Ezh2Y641F mutation in determining its oncogenic activity. The varied temporal contexts result in distinct downstream changes that govern the ultimate oncogenic impact of EZH2 mutations.

overall_design: RNA sequencing was performed on pro and pre pro B cells sorted from mouse bone marrow, from mice expressing either Ezh2-WT or Ezh2-Y641F under the control of either Mx1-Cre or CD19-Cre (n=3-4 biological replicates per group).

last: Zimmerman

first: Samantha

last: Nixon

first: Sofia

last: Smith

first: Jie-Yu

last: Liu

first: Chad

last: Torrice


title: Biallelic BRF2 mutations cause syndromic immunodeficiency and change RNA polymerase III-mediated transcription

status: Public on Nov 06 2024

city: Seoul

first: Seungbok

last: Lee

address: 101, Daehak-ro, Jongno-gu

department: Department of Genomic Medicine

country: South Korea

institute: Seoul National University Hospital

summary: TFIIB-related factor 2 (BRF2) crucially recruits RNA polymerase III (Pol III) to type III promoters containing a TATA box. These promoters encompass crucial components such as U6 spliceosomal RNA, tRNA processing enzyme RNase P, and selenocysteine tRNA. The results on cancer occurrence due to overexpression of BRF2 are known, but genetic disorders caused by mutations in BRF2 are still not well understood. Here, we first identified biallelic BRF2 variants exhibiting defective RNA Pol III activity to type III promoter in a familial patient presenting multiple anomalous features and primary immunodeficiency.

overall_design: Depletion of BRF2 was carried out by small interfering RNAs (siRNAs) against human BRF2 (siRNA ID: 55290) and a negative control.


title: Targeting SUMO2 reverses aberrant epigenetic rewiring driven by SS18::SSX fusion oncoproteins and impairs sarcomagenesis [RNA-seq]

city: La Jolla

first: Aniruddha

middle: J.

last: Deshpande

state: CA

address: 10901 North Torrey Pines Road

department: Cancer Genome and Epigenetics Program

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: Synovial sarcoma (SySa) is an aggressive soft tissue sarcoma with an urgent need to develop targeted therapies. Here, we exploited specific vulnerabilities created by transcriptional rewiring by the fusion protein SS18::SSX, the sole oncogenic driver in SySa. To uncover genes that are selectively essential for the fitness of SySa cells compared to other tumor cell lines, we mined the Cancer-Dependency-Map data. Targeted CRISPR library screening of SySa-selective candidates revealed that the small ubiquitin-like modifier 2 (SUMO2) constituted one of the strongest dependencies both in vitro and in vivo. TAK-981, a clinical-stage small-molecule SUMO2 inhibitor potently suppressed growth and colony-forming ability. Transcriptomic profiling showed that SUMO2 inhibition elicited a profound reversal of the gene expression program orchestrated by SS18::SSX fusion. Further, genetic depletion or SUMO2 inhibition reduced global expression levels and chromatin occupancy of the SS18::SSX fusion protein with a concomitant reduction in histone 2A lysine 119 ubiquitination (H2AK119ub), an epigenetic mark facilitating SySa pathogenesis. Taken together, our study identifies SUMO2 as a novel, selective vulnerability in synovial sarcoma, suggesting new avenues for targeted treatment of soft tissue tumors.

overall_design: Gene expression comparisons of TAK-981 treated versus DMSO treated SYO1 and HS-SY-II celllines using RNA-seq.

first: Rema

last: Iyer

first: Anagha


title: Guidance for the design and analysis of cell-type specific epigenetic epidemiology studies

city: Exeter

first: Jonathan

last: Mill

address: RILD Building, RD&E Hospital

department: Medical School

institute: University of Exeter

type: Methylation profiling by genome tiling array

summary: Recent studies on the role of epigenetics in complex disease have focused primarily on DNA methylation. As genome-wide patterns of DNA methylation are largely determined by cell type, analyses of bulk tissues, composed of a heterogeneous mix of cell types, limits the ability to identify both the specific loci affected by disease associated differences and the cell type within which these changes occur. Cell-specific datasets now make it possible to identify DNA methylation differences associated with disease in specific cell types. Critically, the analytical framework for these differ from the traditional bulk tissue approach, as the statistical method needs to characterise whether the difference affects multiple cell types or is specific to a particular cell-type. In this manuscript, we evaluate the effects on study design, data preprocessing and statistical analysis for cell-specific studies of DNAm, particularly for scenarios where multiple cell types are considered. For this study we take advantage of a large set of DNA methylation profiles (n = 751) obtained from five different purified cell populations isolated from human prefrontal cortex nuclei samples.

overall_design: Post-mortem tissue from 287 adult donors (aged 18-108 years old) were processed using a FANS protocol developed by our group (Policicchio et al. 2020) into up to four purified populations of cells per individual. After stringent quality control of the DNA methylation data 751 nuclei samples were retained: 218 Total, 164 DoubleNeg, 182 NeuNPos, 168 Sox10Pos, 12 IRF8Pos and 7 TripleNeg nuclei samples.

first: Eilis

last: Hannon

first: Emma

last: Dempster

first: Alice

last: Franklin

last: Walker


title: Transcriptomic changes in THP1 human AML cell line on PHF6 knockout, PHF6R274Q mutation, PHIP knockout, and double knockout of PHF6 and PHIP compared to wildtype cells

first: Vikram

last: Paralkar

overall_design: RNA-Seq of wildtype, PHF6 knockout, PHF6R274Q mutant, PHIP knockout, and PHF6/PHIP double-knockout THP1 AML cells that were clonally selected and expanded after Cas9/RNP and sgRNA transfection

last: Pawar


title: Targeting SUMO2 reverses aberrant epigenetic rewiring driven by SS18::SSX fusion oncoproteins and impairs sarcomagenesis

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

overall_design: Refer to individual Series


title: Targeting SUMO2 reverses aberrant epigenetic rewiring driven by SS18::SSX fusion oncoproteins and impairs sarcomagenesis [CUT&RUN]

overall_design: CUT&RUN of SS18-SSX fusion protein in DMSO and TAK-981 treated SYO-1 cell line


title: Targeting SUMO2 reverses aberrant epigenetic rewiring driven by SS18::SSX fusion oncoproteins and impairs sarcomagenesis [ChIP-seq]

overall_design: ChIP-seq of H2AK119ub in DMSO and TAK-981 treated SYO-1 cell line


title: Targeting SUMO2 reverses aberrant epigenetic rewiring driven by SS18::SSX fusion oncoproteins and impairs sarcomagenesis [CRISPR Screening]

overall_design: Cell fitness assessment of HS-SY-II Cas9 cellline during day0, in vitro culture day14, and cellline derived xenograft (CDX) in mouse.


title: Gene expression profile of patient with biallelic BRF2 mutation

status: Public on Nov 05 2024

first: Haeyoon

last: KWON

address: 103 Daehak-ro

institute: Seoul National University College of Medicine

summary: We performed single-cell RNA sequencing (scRNA-seq) on whole blood cells from a patient with biallelic BRF2 variants (c.782C>T and c.379C>T), exhibiting defective RNA polymerase III activity. The patient presented with recurrent infections, hypogammaglobulinemia, and was later diagnosed with low-grade B cell lymphoma. Our scRNA-seq analysis revealed alterations in gene expression related to BRF2-dependent Pol III transcription, particularly affecting redox genes, including GPX1 and GPX4.

overall_design:
Peripheral blood mononuclear cells (PBMCs) were isolated from a patient with biallelic BRF2 mutations and from four age-matched pediatric healthy controls obtained from an independent study. All samples were processed using the 10X Genomics Chromium platform (5' HT v2) for single-cell RNA sequencing. After sequencing, scRNA-seq data were aligned to the GRCh38 reference using Cell Ranger (v7.1.0). Demultiplexing was performed with Demuxafy based on SNP array data. Ambient RNA contamination was corrected using SoupX, and doublets were removed with DoubletFinder. Following quality control in Seurat, all samples were merged, batch-corrected with Harmony, and subjected to UMAP for dimensionality reduction and Louvain clustering. Differential expression and gene set enrichment analyses were performed to explore transcriptional signatures associated with BRF2 deficiency.

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

UPDATE: [Aug-12-2025] The processed data were updated.

last: Kwon

first: Seobin

last: Yoon

first: Soyoung

last: Jeong

first: Christine Suh-Yun

last: Joh

first: Hyun Je

last: Kim

first: Keun P

first: Jong-Hee

last: Chae


title: Cytokines reprogram airway sensory neurons in asthma

status: Public on Nov 04 2024

city: Montréal

first: Theo

last: Crosson

state: Quebec

address: 2900 Boulevard Edouard Montpetit

country: Canada

institute: Université de Montréal

summary: Nociceptor neurons play a crucial role in maintaining the body’s homeostasis by detecting and responding to potential dangers in the environment. However, this function can be detrimental during allergic reactions, since vagal nociceptors can contribute to immune cell infiltration, bronchial hypersensitivity, and mucus imbalance, in addition to causing pain and coughing. Despite this, the specific mechanisms by which nociceptors acquire pro-inflammatory characteristics during allergic reactions are not yet fully understood. In this study, we aimed to investigate the molecular profile of airway nociceptor neurons during allergic airway inflammation and identify the signals driving such reprogramming. Using retrograde tracing and lineage reporting, we identified a unique class of inflammatory vagal nociceptor neurons that exclusively innervate the airways. In the ovalbumin mouse model of airway inflammation, these neurons undergo significant reprogramming characterized by the upregulation of the NPY receptor Npy1r. A screening of cytokines and neurotrophins revealed that IL-1β, IL-13 and BDNF drive part of this reprogramming. IL-13 triggered Npy1r overexpression in nociceptors via the JAK/STAT6 pathway. In parallel, sympathetic neurons and macrophages release NPY in the bronchoalveolar fluid of asthmatic mice, which limits the excitability of nociceptor neurons. Single-cell RNA sequencing of lung immune cells has revealed that a cell-specific knockout of Npy1r in nociceptor neurons in asthmatic mice leads to an increase in airway inflammation mediated by T cells. Opposite findings were observed in asthmatic mice in which nociceptor neurons were chemically ablated. In summary, allergic airway inflammation reprograms airway nociceptor neurons to acquire a pro-inflammatory phenotype, while a compensatory mechanism involving NPY1R limits nociceptor neurons’ activity.

overall_design: Mice in which NPY1R was floxed in nociceptor neurons (sample 1;3;5; n=3) and littermate controls (samples 2;4;6; n=3), as well as C57BL6 mice depleted of peptidergic nociceptors with RTX (samples 14;16; n=2) or not (samples 13;15; n=2) underwent the classic ovalbumin asthma protocol (samples 1-6 and 13-16). C57BL6 mice treated with PBS were used for naive controls (sample 9; n=1).  Mice lungs were harvested (day 18), minced with a razor blade, digested in Collagenase IV (1.6mg/ml) + DNAse I (10ug/ml) in DMEM buffer supplemented with Hepes (10mM) for 30 min. Lungs were triturated with a 1mL pipette and cell suspensions were filtered (40um). 2 different mice were pooled for each sample. RBC were lysed before staining with viability dye and anti-CD45. 500000 live immune cells were sorted on a FACS ARIA III (BD) and harvested in collection buffer (PBS+ 0.04% BSA + 50% FBS). Cells were then fixed, before single cell library preparation using Chromium 10x fixed RNA kits and instructions (#PN-1000414 and #PN-1000497). Libraries were subsequently sequenced on Illumina Novaseq X.


title: Transcriptome changes associated with targeting mTORC2 in lung squamous cell carcinoma

status: Public on Oct 31 2024

city: Nashville

first: Jin

last: Chen

state: Tennessee

address: T-3207E Medical Center North, 1161 21st Avenue South

institute: Vanderbilt University Medical Center

summary: Lung squamous cell carcinoma (LUSC) represents 30% of NSCLC and is associated with high mortality and a lack of therapies. Targeted therapies for lung adenocarcinoma (LUAD) improve overall survival, but such advances have not been made for treatment of LUSC irrespective of frequent molecular abnormalities. Immune checkpoint inhibitor therapies have achieved some success in LUSC patients. However, most patients do not respond adequately to such treatment, thereby patients are left with fewer specific treatment options. Exploring vulnerabilities in NSCLC, we showed that a high percentage of LUSC patients bear genetic alterations in the PI3K-mTOR-AKT signaling pathway. Loss of function of mTORC2 in LUSC cells inhibits glycolysis and lactate secretion in cultured cells and tumor growth in vivo.  The goal of this study was to investigate how targeting mTORC2 impacts LUSC and the tumor microenvironment, which can be harness for therapeutic options.

overall_design: Control (WT) or mLST8 knockout (KO) human lung squamous cell carcinomas were analyzed for gene expression changes. Three biological replicates were included in the analysis, which were generated from independent experiments.

first: Verra

last: Ngwa


title: Stem cell transcriptional profiles from mouse subspecies reveal cis-regulatory evolution at translation genes

city: Berkeley

first: Rachel

middle: B

last: Brem

address: 321 Koshland Hall

department: Plant and Microbial Biology

institute: UC Berkeley

summary: A key goal of evolutionary genomics is to harness molecular data to draw inferences about selective forces that have acted on genomes. The field progresses in large part through the development of advanced molecular-evolution analysis methods. Here we explored the intersection between classical sequence-based tests for selection and an empirical expression-based approach, using stem cells from Mus musculus subspecies as a model. Using a test of directional, cis-regulatory evolution across genes in pathways, we discovered a unique program of induction of translation genes in stem cells of the Southeast Asian mouse M. m. castaneus relative to its sister taxa. We then mined population-genomic sequences to pursue underlying regulatory mechanisms for this expression divergence, finding robust evidence for alleles unique to M. m. castaneus at the upstream regions of the translation genes. We interpret our data under a model of changes in lineage-specific pressures across Mus musculus in stem cells with high translational capacity. Our findings underscore the rigor of integrating expression and sequence-based methods to generate hypotheses about evolutionary events from long ago.

sample_organism: Mus musculus domesticus x Mus musculus castaneus

overall_design: To further investigate gene expression patterns observed in previously published F1 hybrid stem cells, we sequenced undifferentiated pluripotent stem cells from a C57BL/6 line and a CAST/EiJ line.

first: N

last: Simon

first: Y

first: J

last: Gribnau

first: D

last: Bautista

last: Dutton

first: R


title: Cell type-specific purifying selection of synonymous mitochondrial DNA variation

city: New York

first: Caleb

last: Lareau

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering


title: Synonymous mitochondrial DNA variation impairs CD8 T cell fate via codon affinity [PBMC scATAC]

summary: Somatic variation contributes to biological heterogeneity by modulating the cellular proclivity to differentiate, expand, adapt, or die. While large-scale sequencing efforts have revealed the foundational role of somatic variants to drive human tumor evolution, our understanding of the contribution of somatic variation to modulate cellular fitness in non-malignant contexts remains understudied. Here, we identify a somatic synonymous variant (m.7076A>G) in the mitochondrial DNA (mtDNA) encoded cytochrome c-oxidase subunit 1 gene (COX1), which was present at homoplasmy in 47% of immune cells from a healthy donor. Using single-cell multi-omics, we discover highly specific selection against the m.7076G mutant allele in the CD8+ effector memory T cell compartment in vivo, reminiscent of selection observed for pathogenic mtDNA alleles and indicative of lineage-specific metabolic vulnerabilities. Due to the limited transfer RNA (tRNA) pool in mitochondria, the m.7076G mutant allele requires wobble-dependent translation whereas the wildtype m.7076A allele can translate via Watson-Crick-Franklin (WCF) base-pairing. Mitochondrial ribosome profiling revealed that the synonymous m.7076G mutant allele altered codon-anticodon affinity by 33% at the wobble position, stalling translation at the glycine residue within COX1 encoded at m.7076. Leveraging population-based sequencing analyses, we identify evidence of synonymous somatic variants in tumor genomes and dozens of germline variants associated with complex diseases, suggesting broad functional effects of synonymous variation altering codon affinity across the mitochondrial genome. Together, these results provide a new ontogeny for mitochondrial genetic variation and elucidate a framework whereby somatic variation can impact cell state transitions in a lineage-specific manner.

overall_design: 5 PBMC draws were taken from a healthy donor over the course of ~5 months


title: The competition between splicing and 3′ processing shapes the human transcriptome

status: Public on Oct 28 2024

city: Irvine

first: Yongsheng

last: Shi

state: California

address: 811 Health Sciences Road, Medical Sciences B Room 262

department: Microbiology & Molecular Genetics

institute: UC Irvine

summary: Eukaryotic pre-mRNA processing steps, including splicing and 3′ processing, are tightly coordinated, but the underlying mechanisms remain poorly understood. Previous studies proposed that the splicing factor U1 snRNP inhibits 3′ processing at intronic polyadenylation (IPA) sites through a splicing-independent mechanism, called telescripting. However, we found that global or gene-specific perturbation of splicing by targeting multiple splicing factors, including U1 snRNP, U2 snRNP, U2AF, and SF3b led to activation of 3′ processing at IPA sites. Inhibiting different splicing factors activated overlapping and distinct IPA sites and such specificity was determined, at least in part, by alterations in RNA polymerase II elongation and termination. Conversely, we showed that blocking pre-mRNA 3′ processing promoted splicing globally. These results strongly suggest that splicing and 3′ processing are competing processes that shape the transcriptome. Finally, as splicing inhibition-induced shifts to IPA site usage can lead to gene inactivation, including tumor suppressor genes, the use of general splicing inhibitors to treat human diseases may pose a significant risk.

overall_design:
Examination of 30 samples by PAS-seq, a type of 3′ end mRNA-sequencing. There are 3 biological replicates of 50uM control AMO treatment, 3 biological replicates of 50uM U2 AMO treatment, 3 biological replicates of control shRNA treatment, 3 biological replicates of U2AF1 shRNA treatment, 3 biological replicates of U2AF2 shRNA treatment, 3 biological replicates of DMSO treatment, 3 biological replicates of OTS964 (OTS) treatment, 3 biological replicates of Pladienolide B (PB) treatment, 3 biological replicates of 25uM control AMO treatment, and 3 biological replicates of 25uM U1 AMO treatment. All samples were prepared from HEK293T cells.

Examination of 42 samples by 4sU-seq. There are 3 biological replicates of 50uM control AMO treatment, 3 biological replicates of 50uM U2 AMO treatment, 3 biological replicates of control shRNA treatment, 3 biological replicates of U2AF1 shRNA treatment, 3 biological replicates of U2AF2 shRNA treatment, 3 biological replicates of DMSO treatment, 3 biological replicates of OTS964 (OTS) treatment, 3 biological replicates of Pladienolide B (PB) treatment, 3 biological replicates of 25uM control AMO treatment, and 3 biological replicates of 25uM U1 AMO treatment. All samples were prepared from wild-type HEK293T cells. In addition, we generated a HEK293T cell line in which a FKBP12 F36V-degron was fused to the N-terminus of INTS11 via CRISPR/Cas9. We performed 4sU-seq in this cell line following treatment with 25 µM control AMO + DMSO (3 replicates), 25 µM control AMO + dTAG to induce INTS11 degradation (3 replicates), 25 µM U1 AMO + DMSO (3 replicates), and 25 µM U1 AMO + dTAG to induce INTS11 degradation (3 replicates).

Examination of 41 samples by mRNA-seq. There are 3 biological replicates of 50uM control AMO treatment, 3 biological replicates of 50uM U2 AMO treatment, 3 biological replicates of control shRNA treatment, 3 biological replicates of U2AF1 shRNA treatment, 3 biological replicates of U2AF2 shRNA treatment, 3 biological replicates of DMSO treatment, 3 biological replicates of OTS964 (OTS) treatment, 3 biological replicates of Pladienolide B (PB) treatment, 3 biological replicates of 25uM control AMO treatment, and 2 biological replicates of 25uM U1 AMO treatment. All samples were prepared from wild-type HEK293T cells. In addition, we generated a HEK293T cell line in which a FKBP12 F36V-degron was fused to the N-terminus of INTS11 via CRISPR/Cas9. We performed mRNA-seq in this cell line following treatment with 25 µM control AMO + DMSO (3 replicates), 25 µM control AMO + dTAG to induce INTS11 degradation (3 replicates), 25 µM U1 AMO + DMSO (3 replicates), and 25 µM U1 AMO + dTAG to induce INTS11 degradation (3 replicates).

first: Lindsey

middle: V

last: Soles


title: Synonymous mitochondrial DNA variation impairs CD8 T cell fate via codon affinity [mitoRiboseq]

overall_design: Two replicates of cell input were prepared to compare input (RNA-seq) to mitochondrial ribosome profiles that were prepared from different fractions along a sucrose gradient (libraries marked 5-9)


title: Scn2a deletion disrupts oligodendroglia function: Implication for myelination, neural circuitry, and auditory hypersensitivity in ASD.

status: Public on Oct 09 2024

city: Ann Arbor

first: Han-Gyu

last: Bae

state: MI

address: 1301 CATHERINE ST

institute: University of Michigan

summary: Autism spectrum disorder (ASD) is characterized by a complex etiology, with genetic determinants significantly influencing its manifestation. Among these, the Scn2a gene emerges as a pivotal player, crucially involved in oligodendrocyte (OL) function. The present study elucidates the underexplored roles of Scn2a in OL functionality, subsequently affecting myelination and auditory neural processes. The results reveal a nuanced interplay between OLs and axons, where Scn2a deletion causes alterations in OL differentiation and myelination. This disruption, in turn, instigates changes in axonal properties and neuronal activities at the single cell level. Furthermore, OL-specific Scn2a deletion compromises the integrity of neural circuitry within auditory pathways, leading to auditory hypersensitivity—a common sensory abnormality observed in ASD. Through transcriptional profiling, we identified alterations in the expression of myelin-associated genes, highlighting the cellular consequences engendered by Scn2a deletion. In summary, the findings of this study provide unprecedented insights into the pathway from Scn2a deletion in OL to sensory abnormalities in ASD, underscoring the integral role of Scn2a-mediated OL myelination in auditory responses. This research thereby provides novel insights into the intricate tapestry of genetic and cellular interactions inherent in ASD.

overall_design: The nuclei of brainstem from 4 mice, 2 cKO and 2 Cont, were isolated. Nuclei were barcorded, and those were used for seuqencing library using PARSE Evercode WT mini kit.

first: Wan-Chen

last: Wu

first: Kaila

last: Nip

first: Elizabeth

last: Gould

first: Jun


title: Synonymous mitochondrial DNA variation impairs CD8 T cell fate via codon affinity [TCR scRNA]

overall_design: T cells were sorted from peripheral blood mononuclear cells and profiled using single-cell sequencing of the gene expression and TCR sequences


title: Limited proteolysis of neutrophil granule proteins by the bacterial protease RgpB 2 depletes neutrophil antimicrobial capacity

status: Public on Oct 08 2024

city: Columbus

first: Juhi

last: Bagaitkar

address: 700 Childrens Dr

institute: Nationwide Childrens.org

summary: Neutrophils are highly abundant in the gingival tissues where they play an essential role in immune homeostasis by preventing microbial invasion. Here, we show that the oral periodontal pathogen Porphyromonas gingivalis utilizes its cysteine proteases (gingipains) to disengage phagosomal antimicrobial capacity without inducing neutrophil apoptosis. Arginine gingipains are a sub-family of trypsin-like proteases produced by P. gingivalis that cleave several host proteins at arginine residues. We found that RgpB action is not limited to the extracellular or plasma membrane-associated host proteins but can proteolytically modify several intracellular proteins in neutrophils. We used 2D-DIGE coupled with mass spectrometry to identify neutrophil proteins susceptible to RgpB-mediated cleavage and determined the impact of these modifications on neutrophil antimicrobial capacity and inflammatory responses. RgpB cleaved several cytoskeletal and cytoplasmic proteins, including metabolic enzymes and antimicrobial proteins such as neutrophil elastase, myeloperoxidase, and proteinase 3 within neutrophil granules. RgpB also directly primed neutrophils, increasing integrin expression and inducing broad transcriptional changes, consistent with proinflammatory reprogramming. However, despite their primed status and augmented inflammatory capacity, RgpB-treated neutrophils were conducive to intracellular bacterial survival due to the reduced activity of granule proteins and oxidative burst. Thus, our data show a previously unknown role for P. gingivalis proteases in the systematic inactivation of neutrophil microbicidal capacity via proteolysis of intracellular proteins.

overall_design: Peripheral neutrophils were obtained from whole blood from healthy human donors using Percoll density gradient. Neutrophils were treated with a vehicle control or purified bacterial protease (RgpB) for 1 h. Following treatment, neutrophils were washed twice with PBS to remove residual RgpB and RNA was exracted. We profiled differenital gene expression to determine how RgpB exposure impacts the inflammatory priming of neutrophils.

first: Kelley

last: Cooper

first: Aleksandra

last: Wielento

first: Savannah

last: Morris

first: Marina

last: Terekhova

first: Carlos

last: Rodriguez-Hernandez

first: Barbara

last: Potempa

first: Katherine

last: Carey

first: Maxim

last: Artyomov

first: Jan


title: Mouse uterine gene expressions during peri-implantation period

city: Bunkyo-ku

first: Shizu

last: Aikawa

state: Tokyo

address: 7-3-1 Hongo

institute: The University of Tokyo

summary: The mouse uterine gene expressions during peri-implantation period at pregnancy day 4 and 6 was investigated by Visium spatial transcriptome.

overall_design: The day when the vaginal plug was detected was considered day 1 of pregnancy. Pregnant mice were euthanized by cervical dislocation on designated days of pregnancy for the evaluation of pregnancy phenotypes and sample collection. On day 4, one uterine horn was flushed with saline to confirm the presence of blastocysts. Embryo attachment sites were observed as blue bands soon after intravenous injection of 1% solution of Chicago blue dye (Sigma-Aldrich) in saline on day6. Collected tissues were snap-frozen. Frozen sections (10 μm) were mounted on gene expression slides and sent to KOTAI Biotechnologies for subsequent procedures. After reaction with Proteinase K for 40 min, the sections were hybridized with spatial tags on the slides and reverse-transcribed in situ. The synthesized cDNAs were subjected to RNA-sequencing using DNBseq (MGI), producing 300 million reads/sample.

first: Yasushi

last: Hirota


title: Chimeric exosomes-derived immunomodulator restoring lymph node microenvironment for sensitizing TNBC immunotherapy

status: Public on Oct 01 2024

city: Shenyang

first: Zhichao

last: Chen

address: 103 Wenhua Road

institute: Shenyang Pharmaceutical University

summary: Immunotherapy is a breakthrough in the treatment of triple-negative breast cancer (TNBC), whereas is effective in a portion of patients. Our clinical studies found that lipid homeostasis imbalance and dendritic cells (DCs) dysfunction contributed to the immunosuppressive microenvironment in the lymph nodes (LNs) of TNBC patients following immunotherapy, which greatly affected the immunotherapeutic efficacy. Building on this, we introduce a chimeric exosomes-derived immunomodulator, EMV@SS-Toy, involving a polysulfide bond-bridged mesoporous silica nanoparticles (SS-MSN) as a reactive oxygen species (ROS) scavenger and responsive carrier nucleus, loading with the (IRE1α-XBP1) inhibitor toyocamycin (Toy) and coating with chimeric exosomes comprising DCs-derived exosomes and Salmonella outer membrane vesicles. This multifaceted immunomodulator can significantly enhance LNs’ homing via homologous targeting and chemokine-guided navigation, enabling a pathological ROS-responsive drug release, dual-stress pathway regulation, thereby restoring and DCs’ function and LNs’ immune microenvironment. As expected, the immunomodulator markedly boosted the responsiveness of TNBC to immunotherapy, exerting potent inhibition on both the primary tumor and metastases and establishing long-term immune surveillance. Our study provides potent directions for translational immunotherapy through optimizing the LNs’ microenvironment in TNBC.

overall_design: To investigate the immunostimulatory potential of engineered extracellular vesicles (EMVs), we treated DC2.4 cells with EMV@SS and performed GO enrichment analysis to identify the immune-related gene expression changes.

first: Mengchi

last: Sun

first: Yuxia

first: Boyan

last: Zhang


title: Human Immune Exhaustion Gene Expression Profile in C7R-CAR and CAR NK cells

status: Public on Sep 30 2024

city: Houston

first: Matthew

last: Dysthe

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary: The purpose of this experiment was two-fold. The first was to examine how the gene expression profile changes over time in C7R-CAR NK cells. C7R is a constitutively active IL-7 receptor that provides persistent activation of STAT5. The second was to examine the differential gene expression in C7R CAR NK cells or CAR NK treated with exogenous IL-15 (exIL15) after 2 weeks of stimulation.

overall_design: There are 9 experimental samples. Total RNA from C7R-GD2.CAR NK cells is represented at two different timepoints, the day 0 timepoint an day 14 timepoint. Each condition is represented by 3 matched donors. Total RNA was isolated at 14 from GD2.CAR NK cells treated with exogenous IL-15 to enable two week comparison of C7R and IL-15 signaling.

first: Robin

last: Parihar


title: Piezo1-mediated Mechanotransduction Shapes ILC2 Translational Activity, Functions, and Lung Pathogenicity

first: MinYeong

last: Lim

address: 103, Daehak-ro, Jongno-gu

department: Department of biomedical scicence

institute: Seoul National University, College of Medicine

summary: Group-2 innate-lymphoid cells (ILC2s) are critical mediators of the type-2 immune responses in multiple lung pathologies. We show that Piezo1, a mechanosensitive ion channel, plays a key role in regulating ILC2 functions by linking mechanical cues to biochemical signaling pathways. Both murine and human ILC2s strongly express Piezo1, and its activation by Yoda1 selectively enhances IL-13 production through calcium influx, which activates the mTOR-S6K pathway. This pathway leads to translational reprogramming, favoring IL-13 translation. Piezo1-deficient in ILC2s impairs this process, reducing IL-13 levels and resulting in attenuated lung inflammation and fibrosis in mouse models of IL-33- or Alternaria alternata-induced airway inflammation and bleomycin-induced fibrosis. These findings position Piezo1 as a critical mediator of ILC2-driven type-2 immune responses and highlight its potential as a therapeutic target for lung diseases characterized by excessive inflammation. This streamlined understanding of Piezo1 function improves focus on its mechanistic role in lung pathology.

overall_design: mRNA profiles of Yoda1- or DMSO- treated mouse lung ILC2s were generating by bulk mRNA seq using a Nova Seq 6000 (Illumina, Inc., USA).

first: Hye Young

last: Kim


title: Comprehensive analysis of human keratinocyte and opportunistic pathogenic Candida interactions

city: Szeged

first: Marton

last: Horvath

state: Csongrád

address: Közép fasor 52.

department: Microbiology

country: Hungary

institute: University of Szeged

summary: In recent years, microbiome studies revealed that Candida species are common colonisers of the human skin. The distribution of species however varies greatly. Although C. parapsilosis is more likely to resemble skin commensals, opinions are divided, and discrepancies are present regarding C. albicans, that is also often associated with cutaneous candidiasis. Therefore, we aimed to thoroughly assess the nature of skin epithelial cell - Candida interactions. To study species-specific host reponses, we examined phagocytosis, cytokine and metabolic responses in different keratinocytes (HaCaT, HPV-KER) along with host cell damage following fungal stimuli. These results suggest that C. albicans triggers an enhanced antifungal response, thus does not closely resembe skin commensals, like C. parapsilosis. Furthermore, HPV-KER might serve as a more applicable tool for studying keratinocyte antifungal responses. To rigorously examine yeast-keratinocyte interactions, we applied two distinct isolates of both C. albicans (SC5314, WO-1) and C. parapsilosis (GA1, CLIB214). Comparison of the two fungi’s virulence revealed that while C. albicans effectively adheres to human keratinocytes and causes subsequent damage, C. parapsilosis is unable to establish lasting physical contact and causes less harm. In terms of keratinocyte response, both cell lines showed significantly enhanced cellular (% phagocytosis), humoral (IL-6, IL-8) and metabolic responses (2-ketoglutaric acid, citric acid, threorine, hypotaurine) to C. albicans strains, while those towards C. parapsilosis remained relatively low or similar to the control condition. Under certain conditions strain preference was also detected. Of the two cell lines, HPV-KER was more sensitive, as besides interspecies differences, intraspecies differences were also measurable.

sample_organism:
Candida albicans
Homo sapiens

platform_organism:
Candida albicans
Homo sapiens

overall_design: During the experiments C. albicans SC5314, WO-1 and C. parapsilosis GA1 and CLIB214 strains, and undifferentiated HPV-KER and HaCaT human keratinocyte cell lines were used. Then, for RNA-extraction, total of 3x 10^5 keratinocytes were seeded per well. Cells were infected with C. parapsilosis CLIB214 (MOI of 1:1) and C. albicans SC5314 (MOI of 1:25) for 12 hours.

first: Ádám

last: Novák

first: Erik

last: Zajta

first: Máté

last: Csikós

first: Emese

last: Halmos

first: Márton

last: Horváth

first: Orsolya

last: Tildy

first: András

last: Szekeres

first: Nikolett

last: Gémes

first: Gábor

last: Szebeni

first: Renáta

last: Tóth

first: Attila

last: Gácser


title: Reproducible lung protective effects of a TGFβR1/ALK5 inhibitor in the bleomycin-induced and spirometry-confirmed mouse model of IPF

status: Public on Sep 27 2024

city: Hørsholm

first: Henrik

last: Hansen

address: Hørsholm Kongevej 11

department: Histology & NGS

country: Denmark

institute: Gubra

summary: Lung RNA-seq analysis was performed on BLEO-IPF mice at 7-42 days. Pulmonary transcriptome signatures of inflammation and fibrosis in BLEO-IPF mice were comparable to reported data in IPF patients.

overall_design: RNA-seq of poly A-enriched RNA isolated from the lung of  BLEO-IPF mice 7, 14, 21, 28, 35, or 42 days after bleomycin administration. Saline-treated mice served as controls.

first: Maja

middle: W

last: Andersen

first: Martin

last: Madsen


title: A Systematic Profiling of the Bos-Taurus Microbiome and Transcriptome by Dietary Supplementation: Relationships Between Differentially Expressed Genes in Major Metabolic Organs and Rumen Bacteria/Fungi

status: Public on Sep 21 2024

city: Chungnamdo

first: Ki Choon Choi

last: Choi

state: Cheonan

address: Seonghwan-eup

department: Grassland and Forage

institute: National Institute of Animal Science

summary: The purpose of this study was to determine the effects of normal diet feed (NF) and alternative diet feed (AF) on animal performance, gene expression in adipose, liver, and muscle, and changes in bacteria and fungi in the rumen of Bos-Taurus using high-throughput sequencing methods. In addition, Interactions between differentially expressed genes (DEGs) in major metabolic organs and rumen bacteria /fungi were studied. A total of 34,360 genes were found to be expressed across all tissues examined based on transcriptome analysis. According to our findings, 34, 36, 28 genes were differentially expressed in the adipose, liver, and muscle tissues, respectively. A majority of DEGs identified were related to osteoclast differentiation, phagosomes, and immune-functions etc. A study of rumen samples revealed that Firmicutes and Bacterioidetes were the most common phyla. An AF diet significantly increased Firmicutes abundance and reduced Bacterioidetes abundance (p< 0.05). Genus-level analysis revealed that the occurrence of Faecalicatena, Intestinimonas, Lachnoclostridium, Faecalicatena, and Intestinimonas was higher (p < 0.05) in animals fed with the AF diet than in animals fed with an NF diet. As for fungi, Neocallimastigomycota accounted for 98.2% of the NF diet and 86.88% of the AF diet. The AF increased the abundance of Orpinomyces (21.15% to 29.7%), Piromyces (0.1% to 1.8%), and other fungi, but reduced the abundance of Neocallimastix (72.0% to 25.2%). Analysis of the correlation between DEGs and microbes showed that rumen bacteria/fungi significantly influenced expression levels of genes in adipose, liver, and muscle tissues

overall_design: Animal feed made from microbially fermented agricultural residues are getting significant attention in recent years to improve animal performance by modulating transcriptomes and microbiomes in the rumen. The purpose of this study was to determine the effects of normal diet feed (NF) and alternative diet feed (AF) on animal performance, gene expression in adipose, liver, and muscle, and changes in bacteria and fungi in the rumen of Bos-Taurus using high-throughput sequencing methods. In addition, Interactions between differentially expressed genes (DEGs) in major metabolic organs and rumen bacteria /fungi were studied

first: Jeong

last: Jung

first: Ki

first: Ilavenil

last: Soundharrajan

first: Dahye


title: Aberrant pace of cortical neuron development in brain organoids from patients with 22q11.2 deletion syndrome and schizophrenia. [scRNA-Seq]

status: Public on Dec 01 2024

first: Bin

last: Xu

address: 1051 Riverside Dr

department: Psychiatry

institute: Columbia University

summary: Adults and children with the 22q11.2 deletion syndrome (22q11.2DS) demonstrate cognitive, social and emotional impairments and markedly increased risk for schizophrenia (SCZ). The alterations in early human brain development resulting from this deletion remain unclear. Here we use organoid models of the developing human cerebral cortex derived from patients with 22q11.2DS and SCZ as well as unaffected controls to identify cell-type-specific developmental abnormalities that result from this genomic lesion. Using RNA-sequencing and follow-up experimental validation we find that loss of genes within the 22q11.2 locus leads to delayed development of cortical neurons.

overall_design: We perfomed gene expression profiling from organoid models of the developing human cerebral cortex. The organoids were derived from 3 hiPSC lines from patients with 22q11.2DS and SCZ as well as 3 unaffected controls matched by sex and age.

first: Sneha

last: Rao

first: Francesco

last: Brundu

first: Joseph

last: Gogos


title: Effets of plant compounds on estrogen receptor positive breast cancer cell line MCF-7

city: New Orleans

first: Elizabeth

middle: Carol

last: Martin

state: LA

address: 1430 Tulane Avenue

department: Medicine

institute: Tulane University

summary: This study was designed to determine the effects of plant derived compounds on the transcriptome of estrogen receptor positive breast cancer. Phytoestrogens are compounds produced by plants that possess weak estrogenic activity. They can be found in a wide variety of plants, including fruits and vegetables, but are most abundant in leguminous plants. Legumes are consumed in almost every diet throughout the world, and in addition to the seeds, many other parts of the plant are also edible, including the pods of some varieties. Soybeans have been demonstrated to contain high concentrations of the isoflavones daidzein and genistein, which are re-sponsible for many of the health benefits of soy. Besides isoflavonoids, flavonoids also exert estrogenic activity, but usually at a much lower level of activity compared to that of isoflavonoids. Also, some flavonoids, including kaempferol and quercetin, canexhibit antiestrogenic activity, with several legumes being a source of these flavo-noids. Coumestrol, a coumestan with high estrogenic activity in cell and animal as-says, is also present in several legume seeds and sprouts. These underutilized plant compounds could hold previously unknown potential for antioxidant activity, anti-inflammation activity, cholesterol lowering ability, and even anticancer activity. The goal of the present study was to identify the effects of plant derived compounds on estrogen receptor positive cell line to determine if the compound possess estrogenic or anti-estrogenic activity, thereby highlighting potential implications on human health through diet.

overall_design: To determine the effect of plant derived compounds on estrogen receptor signaling the MCF-7 breast cancer cell line was treated with 10uM of plant derived compound. Cells were grown in estrogen free media for 48 hours prior to treatment and treatment was for 24 hours prior to RNA seq analysis. Control cells were treated with DMSO

first: Matthew

last: Burow

first: Stephen

last: Boue

first: Muralidharan

last: Anbalagan


status: Public on Sep 19 2024

city: Milano

first: Federico

last: Zambelli

address: Via Giovanni Celoria 26

department: Department of Biosciences

country: Italy

institute: University of Milan

summary:
Effect of thalamic deletion of mouse Sox2, or Nr2f1, on  gene expression in the visual thalamus (dorsolateral geniculate nucleus, dLGN), as described in "SOX2 and NR2F1 coordinate the gene expression program of the early postnatal visual thalamus" (bioRxiv doi number to be updated)
To address the effect of Sox2, or Nr2f1, Cre-mediated thalamic deletion in mouse, on gene expression in the visual thalamus (dLGN), we dissected the dLGN from mutant (Sox2, or Nr2f1) and control mice at postnatal day 0 (P0), for both Sox2 and Nr2f1 mutants. We then performed gene expression analysis by RNAseq.

overall_design: We dissected the dLGN from three pools of three mutant mice each, and three pools of three control mice each, for both Sox2 and Nr2f1 mutants. RNA from snap-frozen dLGNs was extracted with the RNeasy Micro Kit (QIAGEN), as described in detail in the paper, and

first: Giulio

last: Pavesi

first: Sara

last: Mercurio

first: Linda

last: Serra

first: Silvia

last: Nicolis


title: L-rhamnose globally changes the transcriptome of planktonic and biofilm Escherichia coli cells and modulates biofilm growth

status: Public on Sep 17 2024

city: Oberlin

first: Lisa

last: Ryno

state: Ohio

address: 119 Woodland St

department: Chemistry and Biochemistry

institute: Oberlin College

summary: L-rhamnose, a naturally abundant sugar, plays diverse biological roles in bacteria, influencing biofilm formation and pathogenesis. This study investigates the global impact of L-rhamnose on the transcriptome and biofilm formation of PHL628 E. coli under various experimental conditions. We compared growth in planktonic and biofilm states in rich (LB) and minimal (M9) media at 28 °C and 37 °C, with varying concentrations of L-rhamnose or D-glucose as a control. Our results reveal that L-rhamnose significantly affects growth kinetics and biofilm formation, particularly reducing biofilm growth in rich media at 37 °C. Transcriptomic analysis through RNA-seq showed that L-rhamnose modulates gene expression differently depending on the temperature and media conditions, promoting a planktonic state by upregulating genes involved in rhamnose transport and metabolism and downregulating genes related to adhesion and biofilm formation. These findings highlight the nuanced role of L-rhamnose in bacterial adaptation and survival, providing insights for potential applications in controlling biofilm-associated infections and industrial biofilm management.

overall_design: PHL628 E. coli cells were grown in rich (LB) or minimal (M9) media supplemented with either L-rhamnose at 0.5% (w/w), no sugar (0%, LB samples), or 0.5% (w/w) D-glucose (M9 samples).  Cells were grown at either 28 C or 37 C and three biological replicates of planktonic and biofilm samples of each experimental condition type were harvested (16 conditions, 48 samples total).

first: Charlotte

last: Hantus

first: Isabella

middle: J

last: Moppel

first: Jenna

last: Frizzell

first: Anna

last: Francis

first: Kyogo

last: Nagashima


title: A multivalent mRNA vaccine elicits robust immune responses and confers protection in a murine model of monkeypox virus infection

status: Public on Sep 15 2024

city: Shenzhen

first: Yansheng

last: Li

address: 3002 Sungang West Road, Futian District

institute: Shenzhen Second People's Hospital

summary: We developed two multivalent mRNA vaccines that induced strong immune responses and provided protection against monkeypox virus in mice. Additionally, we used single-cell RNA sequencing and V(D)J sequencing to explore the postvaccination immune landscape at the single-cell level and revealed B-cell receptor and T-cell receptor diversity, gene rearrangement, and predicted CDR3 motifs, systematically exploring the post-vaccination immune landscape at the single-cell level. These findings are poised to guide future vaccine design and present an innovative clinical strategy against monkeypox and orthopoxvirus outbreaks.

overall_design: We developed two multivalent mRNA vaccine candidates, AAL and AALI. Using a mouse infection model established with Clade IIb MPXV isolated from clinical patients, we employed single-cell RNA sequencing (scRNA-seq) and V(D)J sequencing to investigate the transcriptional and immune landscapes of B and T cells following vaccination.

first: Lin

last: Cheng

first: Lixu

last: Jiang

first: Zhuohuan

first: Jing

last: Rao

first: Tong

last: Wu

first: Fangyan

last: Zhang

first: Baocai

last: Xie

first: Yu

last: He

first: Lianrong

last: Wang

first: Zheng

first: Shi

last: Chen


title: Gene expression responses to oxygen challenge in a panel of human brain organoids

status: Public on Sep 05 2024

city: Chicago

first: Yoav

last: Gilad

state: IL

department: Genetic Medicine

institute: University of Chicago

summary: The human brain is highly sensitive to oxygen availability, and hypoxia is a common risk factor for neurological and cognitive traits throughout life.  Hypoxia exerts distinct effects on different brain cell types, many of which involve changes in gene expression.  We used brain organoids derived from genotyped human iPSC lines to characterize gene expression at single-cell resolutions under normoxic conditions and both hypoxic and hyperoxic challenges.

overall_design: Brain organoids were differentiated from 21 Yoruba iPSC lines. After 7 weeks of in vitro culture, organoids were adapted to normoxic (10% oxygen) conditions for one week prior to sample collection.  After 8 weeks in culture, organoids were acutely exposed to 24 hours of hypoxia (1% oxygen) or hyperoxia (atmospheric 21% oxygen).  Organoids were then dissociated and lines were pooled for single-cell RNA-seq processing using the 10x Genomics HT v3.1 kit.  Data collection was performed in two separate batches, with 16 lines in batch 1, 7 lines in batch 2, and 2 lines common to both.

first: Benjamin

middle: D

last: Umans


title: Gene expression profiling of WT and Aldh1a1 KO mouse lung tissues

status: Public on Sep 16 2024

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

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

summary: To explore potential impact of Aldh1a1 deficiency in the retinoic acid signaling in the lung, gene expression levels were compared between wildtype and Aldh1a1 deficient lung tissues.  The expression levels of retinoic acid responsive genes were very similar between wildtype and Aldh1a1 deficient lungs, suggesting that Aldh1a1 deficiency has minimal impact on retinoic acid signaling.

overall_design: Lung tissues were isolated from two mice per group (Aldh1a1+/+ and Aldh1a1-/-) and enzymatically digested. Extracted and purified total RNA samples were used for RNA-seq analysis.

first: Yasutaka

last: Okabe

first: Noriko

last: Shinjyo