title: Inhibition of DEK contributes to the tolerance of replication stress and restores HSC function in Fanconi anemia (5-CUT-Tag)

overall_design: HSCs (CD48-CD150+LSK) from DekCon and DekTg mice were sorted and cultured with DMSO or Hydroxyurea (HU, 100 µM) for 48 h, followed by H3K27ac CUT&Tag-seq


title: Inhibition of DEK contributes to the tolerance of replication stress and restores HSC function in Fanconi anemia (2-ATAC)

status: Public on Jan 03 2025

city: Chongqing

first: Zhe

last: Chen

address: 1 Yixueyuan Road, Yuzhong District

country: China

institute: Chongqing Medical University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Replication stress drives functional decline in HSCs and is a major driver of BM failure in Fanconi anemia (FA). At present, how HSCs respond and counteract replication stress remains largely unknown. Using integrated multi-omics, we demonstrate that global chromatin relaxation is a prerequisite for the activation of stress-responsive genes and replication fork stabilization/progression in HSCs under replication stress. The reduced DEK (a chromatin architectural protein) contributes to the chromatin relaxation in HSCs, whereas DEK-overexpressed HSCs are confronted with a strong replication challenge, resulting in impaired HSC maintenance and hematopoiesis. Fancd2 deletion induces DEK expression and causes replication stress in HSCs, while haploinsufficiency of DEK promotes chromatin opening in Fancd2-deficient HSCs and substantially recovers HSC function. Notably, DEK expression is abnormally up-regulated in bone marrow (BM) CD34+ cells from FA patients. Inhibition of DEK significantly restores the proliferation capacity in vitro and engraftment in vivo of BM CD34+ cells from FA patients. At the molecular level, we identify that the transcriptional factor ATF2 directly promotes DEK transcription, mainly relying on the phosphorylated ATF2 (Thr69/71). Wild-type HSCs reduces DEK expression to counteract replication stress through the ATR kinase to phosphorylate ATF2 at Ser490/498. However, Fancd2 deficiency induces hyper-phosphorylation of p38 that further phosphorylates ATF2 at Thr69/71, causing DEK accumulation in HSCs. Collectively, our findings provide the first evidence of a functional link between chromatin relaxation and replication stress tolerance in HSCs, and highlight DEK as a potential molecular target for FA.

overall_design: HSCs (CD48-CD150+LSK) from wild-type C57BL/6J mice were sorted and cultured with DMSO, Gemcitabine (Gem, 0.5 µM), or Hydroxyurea (HU, 100 µM) for 48 h, followed by ATAC-seq


title: Inhibition of DEK contributes to the tolerance of replication stress and restores HSC function in Fanconi anemia (1-RNA)

type: Expression profiling by high throughput sequencing

overall_design: HSCs (CD48-CD150+LSK) from wild-type C57BL/6J mice were sorted and cultured with DMSO, Gemcitabine (Gem, 0.5 µM), or Hydroxyurea (HU, 100 µM) for 48 h, followed by RNA-seq


title: Inhibition of DEK contributes to the tolerance of replication stress and restores HSC function in Fanconi anemia [11-ATAC]

overall_design: HPCs (Lin-Sca-1-c-Kit+) from DekCon and DekTg mice were sorted and cultured with DMSO or Hydroxyurea (HU, 100 µM) for 48 h, followed by ATAC-seq


title: LncRNA CARINH regulates expression and function of innate transcription factor IRF1 in macrophages [RNA-Seq 2]

city: New York City

first: Coen

last: van Solingen

state: New York

address: 435 E30th street, Science Building 723T, Science Building 723T

department: Cardiology/Medicine

country: USA

institute: NYU School of Medicine

summary: The antisense lncRNA CARINH acts as an additional regulatory layer of antiviral immunity through coordinated regulation of the transcription factor IRF1 and downstream interferon-stimulated genes.

overall_design: Mice were inoculated with influenza strain PR8 and were euthanized 4 days later. Lungs were harvested and snapfrozen. Four mice of each groups were used.

first: Yannick

last: Cyr

first: Florencia

last: Schlamp

first: Kathryn

middle: J

last: Moore


title: Suppression of inflammaging prolongs hematopoietic healthspan [dataset 4]

city: New York

first: David

last: Redmond

address: 1300 York Avenue

institute: Weill Cornell Medicine

summary: The impact of Thbs1 gene deletion on BM MSC activity during physiological aging is unknown. In this experiment, RNA Seq analysis was performed on BM MSCs derived from aged (18 month-old) Thbs1 knockout mice. MSCs derived from young (3 month-old) and aged (18 month-old) control mice were used as controls for comparison.

overall_design: Comparative gene expression profiling analysis of BM MSCs derived from aged Thbs1 knockout mice.

first: Pradeep

last: Ramalingam

first: Michael

last: Poulos

first: Jason

last: Butler


title: Suppression of inflammaging prolongs hematopoietic healthspan [dataset 5]

summary: The impact of Thbs1 gene deletion on BMEC activity during physiological aging is unknown. In this experiment, RNA Seq analysis was performed on BMECs derived from aged (18 month-old) Thbs1 knockout mice. BMECs derived from young (3 month-old) and aged (18 month-old) control mice were used as controls for comparison.

overall_design: Comparative gene expression profiling analysis of BMECs derived from aged Thbs1 knockout mice.


title: Suppression of inflammaging prolongs hematopoietic healthspan [dataset 6]

summary: The impact of recombinant Thbs1 (rThbs1) on HSC activity is unknown. In this experiment, RNA Seq analysis was performed on BM HSCs derived from young (4 month-old) control mice that were cultured ex vivo for 11 days in the presence rThbs1 (500 ng/mL) in the presence of a CD36 neutralizing antibody or its isotype control.

overall_design: Comparative gene expression profiling analysis of BM HSCs cultured in the presence of recombinant Thbs1 and a neutralizing antibody targeting CD36.


title: Suppression of inflammaging prolongs hematopoietic healthspan [dataset 3]

summary: The impact of Thbs1 gene deletion on HSC activity during physiological aging is unknown. In this experiment, RNA Seq analysis was performed on BM HSCs derived from aged (18 month-old) Thbs1 knockout mice. HSCs derived from young (3 month-old) and aged (18 month-old) control mice were used as controls for comparison.

overall_design: Comparative gene expression profiling analysis of BM HSCs derived from aged Thbs1 knockout mice.


title: Suppression of inflammaging prolongs hematopoietic healthspan [dataset 1]

summary: The impact of Thbs1 gene deletion on HSC activity in vivo is unexplored. In this experiment, RNA Seq analysis was performed on BM HSCs derived from young (4 month-old) control and Thbs1 knockout mice to characterize transcriptional alterations resulting from constitutive deletion of Thbs1.

overall_design: Comparative gene expression profiling analysis of BM HSCs derived from control and Thbs1 knockout mice.


title: Bisulfite seq of UHRF1 KO A549 cells

city: Beijing

first: Zhou

last: Xindi

state: Beijing

address: 30 Shuangqing Road

department: School of Medicine

institute: Tsinghua University

type: Methylation profiling by high throughput sequencing

summary: To investigate the funciton of UHRF1 in ICAM1 and pro-inflammatory genes regulaiton, we generate the UHRF1 KO cells and profiled the WGBS.

overall_design: Comaprative bisulfie gene expression profiling analysis of Bisulfite seq data of UHRF1 KO A549 cells versus control A549 cells.

first: Xindi

last: Zhou

first: Yufeng

last: He

first: Deng

last: Pan


title: Inhibition of DEK contributes to the tolerance of replication stress and restores HSC function in Fanconi anemia (10-CUT-Tag)

overall_design: HSCs (CD48-CD150+LSK) from wild-type C57BL/6J mice were sorted , followed by p-ATF2 CUT&Tag-seq


title: Intermittent fasting reduces alpha-synuclein pathology and functional decline in a mouse model of Parkinson’s disease

city: Dresden

first: Björn

middle: H

last: Falkenburger

address: Fetscherstrasse 74

department: Neurology

country: Germany

institute: TU Dresden

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

overall_design: Refer to individual Series


title: Intermittent fasting reduces alpha-synuclein pathology and functional decline in a mouse model of Parkinson’s disease [asyn]

summary: Parkinson’s disease (PD) is an age-related neurodegenerative disorder characterized by the degeneration of the nigrostriatal dopaminergic neurons,  and by intraneuronal accumulation of aggregated α-synuclein (aSyn). Environmental factors contribute significantly to neurodegeneration in patients,  and non-pharmacological interventions are increasingly explored. Among these, caloric restriction and time-restricted feeding have demonstrated beneficial effects  in animal models of neurodegenerative diseases. The ketone body β-hydroxybutyrate (BHB) has been suggested to mediate some of these effects.  In this study, we tested the therapeutic potential of intermittent fasting (IF, every other day feeding) in an aSyn-based mouse model of PD.  IF was initiated four weeks after induction of aSyn pathology. Four weeks of IF mitigated the aSyn-induced degeneration of dopaminergic neurons and axon terminals.  IF also reduced aSyn pathology as reported by staining for phosphorylated aSyn and Triton X-100 solubility.  IF mitigated the aSyn-induced motor phenotype, the decrease in striatal dopamine and the decrease in synaptic markers.  In transcriptomic analysis, we observed a robust modulation of genes involved in inflammation and microglia activation even with just brief IF treatment and without synuclein transduction.  In primary mouse neurons, starvation and treatment with BHB were sufficient to induce autophagy and reduced αSyn pathology.  Taken together, IF might constitute a plausible neuroprotective strategy for patients with Parkinson’s diseases.  BHB-induced autophagy and altered neuroinflammation are pathways that potentially contribute to the protective effect.

overall_design: To investigate to effects of intermitted fasting on mesencephalic signalling in a rAAV-A53T-aSynuclein mouse model of parkinson's disease.  We performed RNA-seq analysis to identify and characterize key pathways.

first: Éva

middle: M

last: Szegő

first: Lennart

last: Höfs

first: Elisabeth

last: Dinter

first: Nadine

last: Bernhardt


title: LncRNA CARINH regulates expression and function of innate transcription factor IRF1 in macrophages [RNA-Seq]

first: Coen

last: van Solingen

overall_design: We used three replicate samples of BMDM cells from WT mice and Carinh-KO mice. Either group treated with IFN for 8 hours or vehicle.


title: Targeting FTO suppresses hepatocellular carcinoma by inhibiting ERBB3 and TUBB4A expression [RNA-seq]

first: Zhe

last: Chen

summary: Fat mass and obesity-associated protein (FTO) is an N6-methyladenosine (m6A) demethylase and plays a critical oncogenic role in various cancers. Here we show that FTO is an effective target in hepatocellular carcinoma (HCC). FTO is highly expressed in clinical patients of HCC and presents as a poor prognostic factor. Genetic depletion of FTO dramatically attenuated HCC progression in vivo. Pharmacological inhibition of FTO by FB23/FB23-2 remarkably suppressed the proliferation and migration of HCC cell lines in vitro, as well as inhibiting the HCC tumorigenicity in xeno-transplanted mice. Mechanistically, FB23-2 suppressed the expression of Erb-b2 receptor tyrosine kinase 3 (ERBB3) and human tubulin beta class Iva (TUBB4A) by increasing the m6A level in these mRNA transcripts. The decreased ERBB3 resulted in inhibited Akt-mTOR signaling that subsequently impaired the proliferation and survival of HCC cells. Moreover, FB23-2 abolished the organization of the tubulin cytoskeleton, while enforced expression of TUBB4A rescued the migration of HCC cells. Collectively, our study demonstrated that FTO plays a critical role in HCC by maintaining the proliferation and migration of cells, and highlights the broad potential of FTO inhibitors for targeting HCC.

overall_design: To find the targets of FB23-2 via inhibiting FTO, MHCC97H cells with FB23-2 (2 μM) treatment for 48 hwere selected for RNA sequencing (RNA-seq) and methylated RNA immunoprecipitation sequencing (MeRIP-seq), DMSO-treated MHCC97H cells as vehicle.


title: RNA seq of ICAM-1 high and low subsets in A549 cells

summary: To investigate the ICAM-1 co-expressed signatures, wild-type A549 cells were stained with anti-ICAM1 antibody and isolate ICAM1-high and ICAM1-low subsets and profiled the transcriptome changes by paired-end RNA seq.

overall_design: Comaprative gene expression profiling analysis of RNA-seq data of A549 ICAM1-high and ICAM1-low subsets.

first: Changhe

last: Li


title: Intermittent fasting reduces alpha-synuclein pathology and functional decline in a mouse model of Parkinson’s disease [sham]

overall_design: To investigate to effects of intermitted fasting on mesencephalic signalling in wild type mice that received a sham surgery.  We performed RNA-seq analysis to identify and characterize key pathways.


title: lncRNA expression profiles of  multiple myeloma

city: Wuhan

first: Chunyan

last: Sun

state: HUBEI

address: 1277 Jiefang Dadao, Wuhan 430022, China

department: Hematology

institute: Wuhan Union Hospital

summary: To further investigate the differential expression lncRNA of multiple myeloma, ten multiple myeloma samples （MM）and three normal donors（NDs）were used for RNA sequencing.

overall_design: Bone marrow CD138+ cells were sorted from multiple myeloma patients and normal individuals. Samples were treated with TRIzol and total RNA was extracted. lncRNA expression profiling was carried out in ten multiple myeloma patients and three controls.


title: Dysregulated ac4C modification of mRNA in a mouse model of early stage Alzheimer's disease.

status: Public on Jan 02 2025

city: shanghai

first: danhong

last: wu

address: 3rd Floor, Building 2, 801 Heqing Road, Shanghai

department: Department of Neurology

institute: Shanghai Fifth People’s Hospital, Fudan University

summary: In this study, ac4C modifications in mRNA were investigated using six-month-old 5×FAD transgenic mice, a widely recognized model of Alzheimer's disease, along with age- and sex-matched wild-type (WT) controls. To elucidate the role of ac4C-modified mRNA in AD, we employed three analytical techniques: acetylated RNA immunoprecipitation sequencing (ac4C-RIP-seq), RNA sequencing (RNA-seq), and proteomic analysis. The first two were used to identify mRNAs carrying ac4C modifications and to quantify mRNA abundance, respectively.

overall_design: acetylated RNA immunoprecipitation -sequancing (acRIP-seq) was used to determine the acetylation modification of mRNA in the hippocampus from 6 month mice (3 5xFAD mice and 3 WT mice). Then IgG- sequancing was used to correct the result of acRIP-seq.

first: Haonan

last: Ji

first: Haiqian

first: Jingbo

last: Qie

first: Wenmei

last: Lu

first: Haitao

last: Gao

first: Danhong

last: Wu


title: C-ATF6 improves EGFR tyrosine kinase inhibitor sensitivity in non-small cell lung cancer via modulation of the calcium homeostasis network.

city: nanjing

first: Qianfan

last: Hu

state: jiangsu

address: nanjing

institute: nanjing medical university

summary: Osimertinib (Osi) is an epidermal growth factor receptor tyrosine kinase inhibitor (EGFR-TKI), and its clinical efficacy is limited due to the emergence of resistance. We found that parental cells undergo a drug-tolerant persister (DTP) state before ultimately achieving acquired resistance. In this study, we restored the specifically dysregulated circular RNA (cATF6) in the DTP state and used it in combination with Osimertinib, finding that it could significantly synergistically target DTP tumor cells. Mechanistically, it mainly disrupted the balance of Ca2+, ultimately leading to the death of DTP cells due to Ca2+ overload. This study reveals the impact of cATF6 on the dynamic balance of calcium ions, which may bring new strategies for epidermal growth factor receptor inhibitors (EGFR-TKIs) to eradicate DTP.

overall_design: HCC827 cells were treated with DMSO or osimertinib for 10 days and subjected to whole transcriptome sequencing. Transcriptome sequencing was performed on HCC827 cells in the EV or overexpression of circRNA-cATF6, as well as in the parental, DTP state, and acquired resistant state.

first: Yuxian

last: Qian

first: Zi

last: Wang


title: Quercetin diminishes scleral ER stress and protein misfolding: High throughput transcriptome analysis in form-deprivation myopia of guinea pigs

city: Shanghai

first: Jibo

last: Zhou

address: Quxi road NO.500, Huangpu district

institute: NINTH PEOPLE'S HOSPITAL SHANGHAI JIAO TONG UNIVERSITY SCHOOL OF MEDICINE

summary: This study aims to verify the involvement of scleral endoplasmic reticulum stress (ERS) in form-deprived myopia (FDM) model of guinea pigs, investigate the therapeutic effects of quercetin (Qcn) on FDM as well as explore the underlying mechanisms in human scleral fibroblast (HSF).

overall_design: RNA-seq：We divede guinea pigs into NC group and FDM group. We collected tissue from the posterior pole of the sclera of three right eyes each from the control and FDM groups on day 28 of induction. And then RNA-seq was performed.

first: Lingfeng

last: Lv

first: Danyang

last: Che

first: Zewei

last: Zhang

first: Weijie

first: Qimin

first: Fang


title: Posttranscriptional Control of Neural Progenitors Temporal Dynamics During Neocortical Development by Syncrip

first: Haoyang

last: Yu

address: 9 Dongdan Santiao, Dongcheng District, Beijing

institute: Peking Union Medical College

summary: The development of the mammalian neocortex is precisely regulated by temporal gene expression, yet the temporal regulatory mechanisms of cortical neurogenesis, particularly how radial glial cells (RGCs) sequentially generate deep to superficial neurons, remain unclear. Here, the hnRNP family member Syncrip (hnRNP Q) is identified as a key modulator of superficial neuronal differentiation in neocortical neurogenesis. Syncrip knockout in RGCs disrupts differentiation and abnormal neuronal localization, ultimately resulting in superficial cortical layer defects as well as learning and memory impairments in mice. Single‐cell RNA sequencing analysis demonstrated that the knockout of Syncrip disrupts the late‐stage neurogenesis, stalling transcriptional progression in RGCs. Mechanistically, Syncrip maintains the transcription of temporal process‐related transcription factors by recruiting stabilization complexes through phase separation, crucially regulating the Notch signaling pathway that determines the fate of RGCs. Furthermore, pathogenic human mutations in Syncrip weaken its phase‐separation capability, failing to form stable complexes normally. Thus, Syncrip acts as a mediator of posttranscriptional regulatory mechanisms, governing the fate progression of RGCs and the advancement of intrinsic temporal programs. This study establishes an intracellular mechanism for posttranscriptional regulation of progressive fate determination in cortical neurogenesis.

overall_design: In this study, we aimed to elucidate Syncrip’s role in E14.5 neural progenitor cells (NPCs) and dorsal cortical development. To achieve this, we performed LACE-seq, RNA-seq, and scRNA-seq. LACE-seq was used to reveal direct RNA targets of Syncrip in cultured NPCs, RNA-seq captured global transcriptomic changes between WT and Syncrip cKO, and scRNA-seq provided single-cell-level insights into cellular diversity and differential gene expression within the developing dorsal telencephalon. By integrating these three datasets, we gained a comprehensive perspective on Syncrip-mediated post-transcriptional regulation, systemic transcriptional shifts, and cell-type-specific effects in the embryonic mouse cortex.

first: Jiarui

first: Xinyi

last: Dou

first: Pengcheng

last: Shu

first: Xiaozhong

last: Peng


title: Pde4b-regulated cAMP signaling pathway in the AUDGABA-S1TrSst circuit underlies acute stress-induced anxiety-like behavior

city: qingdao

first: zhixin

last: xiao

address: ningxia road 308

institute: qingdao university

summary: Acute stress-induced anxiety is an important way for animals to avoid danger. However, neural and molecular mechanisms that underlie control of anxiety behavior are largely elusive. Here, we find acute physical stress activates a large number of neurons in the primary somatosensory cortex, trunk region (S1Tr). Single-cell sequencing reveals the S1Tr c-fos positive neurons activated by acute stress are largely GABAergic somatostatin (Sst) neurons. These S1TrSst neurons activated by acute stress showed desensitization during subsequent anxiety-like behavior tests. Selective inhibition or apoptosis of S1TrSst neurons mimics acute stress effects to induce anxiety. In contrast, selective activation of S1TrSst neurons reduced acute stress-induced anxiety. Furthermore, we demonstrate that S1TrSst cells receive inputs from the secondary auditory cortex, dorsal area (AUD) GABAergic neurons to modulate acute stress-induced anxiety. Finally, from the results of spatial transcriptome sequencing and precise projection-specificity Pde4b protein knockdown strategy, we show that acute stress reduces Pde4b-regulated cyclic adenosine monophosphate (cAMP) signaling pathway activity in the AUDGABA-S1TrSst projections and resulting in a hypoactivity of S1TrSst neurons during subsequent behavioral tests. Our study unveils a neural and molecular mechanism for acute stress-elicited anxiety and affords a theoretical basis for clinical treatment of anxiety disorders.

overall_design: Investigation of neuronal gene expression profiles in the S1Tr brain region of mice following acute stress exposure

first: xiaoya

last: wang

last: zhou

first: xuetong

last: yi

first: xiaoqi

last: zhang

first: qilin

last: wu

first: zhuo

last: li


title: A Vulnerable Subtype of Dopaminergic Neurons Drives Early Motor Deficits in Parkinson’s Disease

city: Seattle

first: Akira

last: Fushiki

state: WA

address: 615 Westlake Avenue North

institute: Allen Institute

summary: In Parkinson's disease, dopaminergic neurons (DANs) in the midbrain gradually degenerate, with ventral substantia nigra pars compacta (SNc) DANs exhibiting greater vulnerability. However, it remains unclear whether specific molecular subtypes of ventral SNc DANs are more susceptible to degeneration in PD, and if they contribute to the early motor symptoms associated with the disease. We identified a subtype of Sox6+ DANs, Anxa1+, which are selectively lost earlier than other DANs, and with a time course that aligns with the development of motor symptoms in MitoPark mice. We generated a knock-in Cre mouse line for Anxa1+ DANs and showed differential anatomical inputs and outputs of this population. Further, we found that the inhibition of transmitter release in Anxa1+ neurons led to bradykinesia and tremor. This study uncovers the existence of a selectively vulnerable subtype of DANs that is sufficient to drive early motor symptoms in Parkinson’s disease.

overall_design: Single-nucleus RNA profiling of the ventral midbrain of MitoPark mice, their littermate controls and C57BL/6 mice at 8, 16, and 24 weeks of age (8 mice in each group; 4 males and 4 females). Two animals were used for each sample. For instance, in RA004, two 8-week-old male MitoPark mice were combined.

first: Rui

last: Costa


title: Astrocytic CREB in nucleus accumbens promotes susceptibility to chronic stress

first: Molly

middle: S

last: Estill

state: NY

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

summary: Increasing evidence implicates astrocytes in stress and depression in both rodent models and human Major Depressive Disorder (MDD). Despite this, little is known about the transcriptional responses to stress of astrocytes within the nucleus accumbens (NAc), a key brain reward region, and their influence on behavioral outcomes. We found a robust transcriptional response in NAc astrocytes to CSDS in stressed mice, with changes seen in both stress-susceptible and stress-resilient animals. Bioinformatic analysis revealed CREB, a transcription factor widely studied in neurons, as one of the top-predicted upstream regulators of the NAc astrocyte transcriptome, with opposite activation states implicated in resilient vs. susceptible mice. Our data demonstrate that the astrocyte transcriptome responds robustly to CSDS and that transcriptional regulation in astrocytes contributes to depressive-like behaviors. A better understanding of transcriptional regulation in astrocytes may reveal unknown molecular mechanisms underlying neuropsychiatric disorders.

overall_design: We used whole cell sorting, RNA-sequencing, and bioinformatic analyses to investigate the NAc astrocyte transcriptome in male mice in response to chronic social defeat stress (CSDS).

first: Leanne

last: Holt

first: Trevonn

last: Gyles

first: Eric

last: Parise

first: Angelica

last: Minier-Toribio

first: Matthew

last: Rivera

first: Tamara

last: Markovic

first: Szu-Ying

last: Yeh

last: Nestler


title: Therapeutic potential of microglial SMEK1 via regulation of H3 lysine 9 lactylation in cerebral ischemia-reperfusion injury

city: Jinan

first: Weiyue

last: Si

address: wenhuaxi road #107

institute: Qilu hospital of Shandong University

summary: Immune responses and neuroinflammation occurring after acute ischemic stroke (AIS) are closely related to brain injury. Histone lactylation is a metabolic stress-related histone modification that participates in the pathogenesis of various diseases. However, the role of histone regulation in cerebral ischemic stroke remains unknown. In this study, a transient middle cerebral artery occlusion (tMCAO/R) model and an oxygen–glucose deprivation and reoxygenation (OGD/R) model were used to simulate in vivo/in vitro ischemia–reperfusion injury. The underlying mechanism of microglial histone lactylation was investigated using microglia-specific SMEK1-overexpressing mice and BV2 cells. The results showed that lactate overload resulted in elevated histone lactylation after AIS. Decreased SMEK1 expression in microglia after ischemic stroke was associated with increased lactate levels and subsequent neuroinflammation. Microglia-specific SMEK1 deficiency in microglia after ischemia can promote lactate production by inhibiting the pyruvate dehydrogenase kinase 3-pyruvate dehydrogenase (PDK3-PDH) pathway. Specifically, H3 lysine 9 lactylation (H3K9la) activated Ldha and Hif-1α transcription in microglia and promoted glycolysis. SMEK1-overexpressing mice exhibited better neurologic recovery after ischemic stroke than control mice. Mechanistically, we provided new evidence that microglial histone lactylation promoted glycolysis in ischemia‒reperfusion injury and elucidated the potential role of SMEK1 as an upstream regulatory molecule in histone lactylation after cerebral ischemia. According to our results, microglial SMEK1 may be potential therapeutic targets for AIS.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for BV2 cells and its KD derivatives (LV1 and NL)

first: Ruonan

last: Duan

first: Chunlin

last: Yang

first: Tong

last: Du

first: Liangkang

last: Li

first: Jing

last: Dong

first: Yang

last: Zhou


title: Functional dissection of metabolic trait-associated variants in steady state and stimulated human skeletal muscle cells [RNA-Seq]

city: Ann Arbor

first: Adelaide

middle: Erin

last: Tovar

state: Michigan

address: 100 Washtenaw Ave

department: Computational Medicine & Bioinformatics

institute: University of Michigan

summary: Type 2 diabetes (T2D) is a common metabolic disorder characterized by dysregulation of glucose metabolism. Genome-wide association studies have defined hundreds of signals associated with T2D and related metabolic traits, most of which are found in noncoding regions. Given their central role in insulin production and glucose homeostasis, much focus has been devoted to investigating T2D-associated genetic variation in pancreatic islets; however, metabolic disease pathogenesis and risk is distributed across other important metabolic tissues, including the liver, adipose, and skeletal muscle. Here, we performed RNA-seq in human skeletal muscle cells in one of four conditions: (1) undifferentiated or differentiated with (2) basal media, (3) media supplemented with the AMP analog 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) to mimic physiological effects of exercise or (4) media containing sodium palmitate which is known to induce insulin resistance. We used these profiles to identify how relevant metabolic stimuli influence transcriptome-wide gene regulation.

overall_design: We collected 15 million LHCN-M2 cells after exposure to one of four conditions: undifferentiated, differentiated, differentiated with 2 mM AICAR or differentiated with 0.5 mM palmitate. We later isolated mRNA-enriched sequencing libraries. We performed paired-end sequencing on an Illumina NovaSeq X instrument.


title: Functional dissection of metabolic trait-associated variants in steady state and stimulated human skeletal muscle cells [1]

summary: Type 2 diabetes (T2D) is a common metabolic disorder characterized by dysregulation of glucose metabolism. Genome-wide association studies have defined hundreds of signals associated with T2D and related metabolic traits, most of which are found in noncoding regions. Given their central role in insulin production and glucose homeostasis, much focus has been devoted to investigating T2D-associated genetic variation in pancreatic islets; however, metabolic disease pathogenesis and risk is distributed across other important metabolic tissues, including the liver, adipose, and skeletal muscle. Here, we used a massively parallel reporter assay (MPRA) to characterize the regulatory activity of T2D-associated variants in human skeletal muscle cells at basal and multiple stimulatory states. We constructed a library of 1,255 oligos spanning 333 metabolic trait-associated variants, half of which were previously characterized using luciferase reporters or in MPRA libraries in any metabolic tissue, and therefore serve as positive controls. We delivered this library to LHCN-M2 human skeletal muscle myocytes in one of four conditions: (1) undifferentiated or differentiated with (2) basal media, (3) media supplemented with the AMP analog 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) to mimic physiological effects of exercise or (4) media containing sodium palmitate which is known to induce insulin resistance.

overall_design: We gathered signal variants relevant to T2D and metabolic traits and designed 198-bp fragment sequences.We cloned these sequences into a modified form of the pMPRA1 vector with 20-bp barcodes. We shuttled this assembled library to the pLentiMPRA vector and generated infectious lentivirus. We infected 15 million LHCN-M2 at an MOI of ~10. We later isolated total RNA and gDNA and generated custom barcode sequencing libraries. We performed paired-end sequencing on an Illumina NovaSeq 6000 instrument.


title: Effects of moderate intensity exercise on liver metabolism in mice based on multi-omics analysis

first: Ting

last: Zhang

address: Dongcheng District

institute: Beijing Municipal Key Laboratory of Child Development and Nutriomics

summary: Physical exercise is beneficial to keep physical and mental health. The molecular mechanisms underlying exercise are still worth exploring.The healthy adult mice after six weeks of moderate-intensity exercise (experimental group) and sedentary mice (control group) were used to perform transcriptomic, proteomic, lactylation modification, and metabolomics analysis. In addition, gene sets related to hypoxia, glycolysis, and fatty acid metabolism were used to aid in the screening of hub genes. The mMCP-counter was employed to evaluate infiltration of immune cells in murine liver tissues.

overall_design: To explore the effects of moderate intensity exercise on protein of lactylation in mouse liver metabolism. The 3 healthy adult mice running for 6 weeks as exercise model and 3 sedentary mice as control were used to perform transcriptomic, proteomic, lactylation-proteomics, and metabolomics analysis.

first: Jiahui

last: Chang

first: Wanyu

last: Wu

first: Ping

last: Qian

first: Zhaoxu

last: Lu

first: Xuejia

last: He

first: Fang

last: Wang


title: Functional dissection of metabolic trait-associated variants in steady state and stimulated human skeletal muscle cells

overall_design: Refer to individual Series


title: Aberrant splicing in Huntington’s disease accompanies disrupted TDP-43 activity and altered m6A RNA modifications [RASL-seq]

city: Irvine

first: Ricardo

last: Miramontes

address: 845 Health Sciences Rd

institute: UC Irvine

summary: Huntington’s disease (HD) is a neurodegenerative disorder caused by a CAG repeat expansion in the first exon of the HTT gene, leading to altered gene expression. However, the mechanisms leading to disrupted RNA processing in HD remain unclear. Here, we identify the RNA-binding TDP-43 and the N6-methyladenosine (m6A) writer protein METTL3 to be upstream regulators of exon skipping in multiple HD systems. Dysregulated nuclear localization of TDP-43 and cytoplasmic accumulation of phosphorylated TDP-43 is shown to be present in HD mice and human brains with TDP-43 co-localizing with HTT nuclear aggregate-like bodies distinct from mutant HTT inclusions and from previously observed TDP-43 pathologies. The binding of TDP-43 onto RNAs encoding HD-associated differentially expressed and aberrantly spliced genes is decreased. Finally, m6A RNA modification is reduced on RNAs abnormally expressed in the striatum from HD R6/2 mouse brain, including at clustered sites adjacent to TDP-43 binding sites. Our evidence supports TDP-43 loss of function coupled with altered m6A modification as a mechanism underlying alternative splicing in HD and highlights the critical nature of TDP-43 loss of function across multiple neurodegenerative diseases.

overall_design: To understand how alternative splicing is altered in HD mouse models, we took the R6/2, Q150, and Q175 HD mouse models and performed RASL-seq with primers spanning short (skipped) and long (not skipped) junctions across splicing sites. We compared the respective mouse to their Wildtype controls. for the Q150 and Q175 we used both heterozygous and homozygous for our experiment.

first: Thai

middle: B

last: Nguyen

first: Leslie

last: Thompson


title: Development of stem cell derived type  alveolar epithelial cells (AEC2s) for pulmonary fibrosis modeling

city: Sejong-si

first: Yubin

last: Han

address: Sejong-ro 2511

department: College of Pharmacy

country: South Korea

institute: Korea University

summary: AEC2s are putatively major cells in development of lung diseases like Idiopathic Pulmonary Disease (IPF). For studying IPF-related phenotypes of AEC2s, We used differentiated AEC2s (diff-AEC2s) with some merits compared to conventional in vitro alveolar cells and bleomycin as a pulmonary fibrosis-inducing agent. With bleomycin treatment for 24 hr, some fibrotic phenotypes, senescent and transtional markers like Ctgf, Lgals3, and Krt8 were elevated with dose-dependent manner in RNA and protein expression. Also, up-regulation of P53 pathway and some irregular cell cycle expreesion were identified with bleomycin treatment.

overall_design: RNA profiling for bleomycin-treated diff-AEC2 to figure out expression of fibrosis-related phenotype in AEC2s.

first: Jun Woo

last: Kim

first: Yong Joo

last: Park


title: Functional dissection of metabolic trait-associated variants in steady state and stimulated human skeletal muscle cells [II]


title: Aberrant splicing in Huntington’s disease accompanies disrupted TDP-43 activity and altered m6A RNA modifications [ISO-seq]

overall_design: To investigate the role of mHTT exon1 on the mouse transcriptome and alternative splicing, here we compared males mice at a highly symptomatic timepoint in the R62 HD mouse model against the non-transgenic control by long-read sequencing with pacbio iso-seq. we microdisected two brain regions, the striatum and cortex, which are areas of interest in Huntington's disease.


title: Molecular cause of the differential activity of Sox8 and Sox10 in oligodendroglial cells

city: Erlangen

first: Michael

last: Wegner

state: Bavaria

address: Fahrstr. 17

department: Institut of Biochemistry

summary: Oligodendroglial cells are responsible for the generation of myelin sheaths in the central nervous system and thereby render rapid saltatory conduction possible. During development, oligodendroglial cells express the three paralogous transcription factors Sox8, Sox9 and Sox10. In mature oligodendrocytes Sox8 and Sox10 expression persists. Whereas Sox9 and Sox10 fulfill important regulatory roles in these cells, Sox8 has only a limited impact on oligodendroglial development and myelination. By replacing Sox10 with Sox8 or Sox9 in the oligodendroglial Oln93 cell line and by comparing expression profiles, we show that Sox8 regulates the same processes as Sox10 and Sox9, but has a substantially lower transcriptional activity under standard culture conditions.

overall_design: To identify differential activity of Sox8 and Sox10 in oligodendroglia, we transduced genome-edited Oln93 cells that lack Sox10  with lentiviruses containing GFP and mouse coding sequences for  Sox8, Sox9 or Sox10. Transduced GFP-postive cells were purified by fluorescence activated cell-sorting and used for RNA preparation. RNA-Seq was performed with the isolated total RNA and comparative gene expression profiles were generated.

first: Verena

last: Dehm

first: Jessica

last: Aprato

first: Matthias

last: Weider


title: RNA-sequencing of LNCaP prostate cancer cells with and without treatment of darolutamide

city: Berlin

first: Andreas

last: Schlicker

address: Muellerstr 178

department: Translational Sciences Oncology Computational Biology

institute: Bayer AG

summary: LNCaP prostate cancer cells were stimulated with the synthetic androgen R1881. RNA-sequencing was performed to identify changes induced by darolutamide treatment on the transcriptome level.

overall_design: Prostate androgen-sensitive cell lines LNCaP were grown for two days in starvation medium prior to treatment with synthetic androgen R1881 at a concentration of 1 nM or R1881 with darolutamide at a concentration of 2 µM. The cells were harvested 22 h post-induction for RNA isolation and sequencing.

first: Schlicker

last: Andreas

first: Bernard

last: Haendler

first: Ekaterina

last: Nevedomskaya


title: Aberrant splicing in Huntington’s disease accompanies disrupted TDP-43 activity and altered m6A RNA modifications [eCLIP-seq]

overall_design:
To investigate the epitranscriptomic landscape in the HD R62 mouse model, we carried out m6A-eCLIP sequencing using Eclipse Bioinnovations's m6A-eCLIP sequencing kit. We used both males and female mice n=4 each per genotype, and dissected out cortex and striatum for downstream library construction.
To investigate TDP-43's RNA targets in the HD R62 mouse model, we carried out m6A-eCLIP sequencing using Eclipse Bioinnovations's RBP-eCLIP sequencing kit. We used both males and female mice n=4 each per genotype, and dissected out cortex and striatum for downstream library construction.
To investigate the effect of TDP-43 knockdown on the m6A landscape we knocked down TDP-43 via ASO followed by m6A-eCLIP seq. n=3 per genotype was used.
Please note that processed data files generated from both input and IP samples are linked to the corresponding IP sample records.


title: Heteromeric Kv1.2 channels counteract persistent sodium currents in proprioceptive DRG neurons

city: Salt Lake City

first: Baldomero

last: Olivera

state: UT

address: 201 Presidents' Cir, Salt Lake City

institute: University of Utah

summary: Voltage-gated potassium channels (VGKCs) comprise one of the largest, most diverse and complex families of ion channels. Approximately 70 genes encode the alpha subunits that form homomeric VGKC channels.  In addition, these subunits can form functional heteromeric channels, thus exponentially increasing the diversity of VGKCs. The functional expression and physiological role of heteromeric K-channels have remained largely unexplored due to the lack of tools to probe their functions. Conotoxins have high affinity and specificity for heteromeric combinations of K-channels and show great promise for elucidating their functions. In this work, using conotoxin kM-RIIIJ as a pharmacological probe, we explore the expression and physiological functions of heteromeric Kv1.2 channels using constellation pharmacology. We report that heteromers of Kv1.2/1.1 are highly expressed in proprioceptive neurons found in the dorsal root ganglion (DRG). Inhibition of Kv1.2/1.1 heteromers leads to an influx of calcium ions, suggesting that these channels regulate neuronal excitability. We also present evidence that Kv1.2/1.1 heteromers counteract persistent sodium currents, and that inhibiting these channels leads to tonic firing of action potentials. Additionally, kM-RIIIJ induces impaired proprioception in mice, uncovering a previously unrecognized physiological role of heteromeric Kv1.2/1.1 channels in proprioceptive sensory neurons of the DRG.

overall_design: Single cell proprioceptive neurons isolated from mouse DRG

first: Walter

last: Markel

first: Raghuraman

last: Shrinivasan

first: Carter

last: Jackson


title: Aberrant splicing in Huntington’s disease accompanies disrupted TDP-43 activity and altered m6A RNA modifications

first: Ricardo

last: Miramontes

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
To investigate the role of mHTT exon1 on the mouse transcriptome, here we compared males and female mice at a highly symptomatic timepoint in the R62 HD mouse model against the non-transgenic control by total RNA-seq. we microdisected two brain regions, the striatum and cortex, which are areas of interest in Huntington's disease.
To investigate the role of TDP-43 on the mouse transcriptome, here we compared male C57Bl/6J  striatums with and without TDP-43 ASO by total RNA-seq
To investigate the role of mHTT  on human neurons enriched for medium spiny neurons that are derived from induced pluripotent stem cells. Further we investigated how TDP-43 knockdown relates to the effect of mHTT by studying the transcriptomic changes via total RNA-seq.

first: Thai

last: Nguyen


title: Comprehensive transcriptome-wide profiling of 5-methylcytosine modifications in lncRNAs/circRNAs/mRNAs in a rat model of traumatic brain injury

city: WuHan

first: zhijun

last: xiang

address: Wuhan

institute: Emergency Center, Zhongnan Hospital of Wuhan University

summary: Traumatic Brain Injury (TBI) poses a major global health challenge, leading to serious repercussions for those affected and imposing considerable financial strains on families and healthcare systems. RNA methylation, especially 5-methylcytosine (m5C), plays a crucial role as an epigenetic modification in regulating RNA at the level of post-transcriptional regulation. However, the impact of TBI on the m5C methylation profile of long noncoding RNAs (lncRNAs) remains unexplored. In the present study, we conducted a thorough transcriptome-wide examination of m5C methylation in lncRNAs in a rat TBI model utilizingMeRIP-Seq. Our findings indicated notable variations in the amount and distribution of m5C methylation in lncRNAs between TBI and control groups, highlighting alterations in the m5C methylation landscape of lncRNAs following TBI. Additionally, we conducted bioinformatic analyses to predict the functions of specifically methylated transcripts. These findings offer fresh perspectives on the epigenetic modifications in lncRNA m5C methylation following TBI, which may contribute to understanding the disease mechanisms and developing targeted therapeutic strategies.

overall_design: In the present study, we conducted a thorough transcriptome-wide examination of m5C methylation in lncRNAs/circRNAs/mRNAs in a rat TBI model utilizingMeRIP-Seq

first: Zhijun

last: Xiang

first: Yixing

last: Luo

first: Jiangtao

last: Yu

first: Haoli

last: MA

first: Yan

last: Zhao


title: Determination of the mechanisms of MCPA resistance in Amaranthus powellii

city: Guelph

first: Isabelle

last: Aicklen

address: 50 Stone Road East

country: Canada

institute: University of Guelph

summary: Resistance to synthetic auxin herbicides was recently confirmed in a population of Amaranthus powellii. Following field studies, an RNA-seq experiment was devised to determine the mechanism of resistance to MCPA (a synthetic auxin herbicide) by comparing the level of gene expression of genes in the auxin pathway between the resistant and a susceptible population of Amaranthus powellii. The results identified several differentially expressed genes (DEGs) in the auxin pathway that were significantly downregulated in the resistant samples indicating that the resistance mechanism may be linked to a target site modification.

overall_design: Young leave tissue samples from four treaments were used for RNA extraction. The four treatments were as follows: resistant treated (501T), resistant untreated (501U), susceptible treated (511T), and susceptible untreated (511U). Treated samples were sprayed with 1225 g a.e./ha of MCPA (a synthetic auxin herbicide). At six hours after application, leaf tissue samples from both treated and untreated plants were sampled for RNA extraction. Samples were aligned to both a reference genome (Amaranthus hybridus) and an assembled de novo transcriptome (Amaranthus powellii) and gene count data was compared between all treatments to identify differentially expressed genes DEGs.

first: Mithila

last: Jugulam

first: Todd

last: Gaines

first: William

last: Kramer

first: Martin

last: Laforest

first: Darren

last: Robinson

first: Peter

last: Sikkema

first: Francois

last: Tardif


title: CCR2 limits inflammatory functions of CD8 TRM cells that impair recognition memory during recovery from WNV encephalitis [scRNA-seq]

city: St. Louis

first: Robyn

last: Klein

state: MO

address: 660 S. Euclid Ave.

institute: Washington University in St. Louis

summary: Central nervous system (CNS) resident memory CD8 T cells (TRM) that express IFN-? have been shown to contribute to neurodegenerative processes, including synapse loss, causing memory impairment. Here, we show that CCR2 deficiency in CD8 TRM that persists within the hippocampus after recovery from CNS infection with West Nile virus (WNV) significantly contributes to poor cognitive outcomes. Using CCR2-deficient mice, we determined that CCR2 expression is not essential for CNS T cell recruitment or virologic control during acute WNV infection. However, transcriptomic analyses of forebrain CCR2+ versus CCR2- CD8 TRM during WNV recovery reveal that CCR2 expression significantly regulates hippocampal CD8 TRM phenotype and function, with increased expression of CD103, granzyme A and IFN-?. Consistent with this, WNV-recovered Cd8acreCcr2fl/fl mice exhibit decreased recognition memory. Our findings highlight CCR2's role in regulating CD8 T cell-mediated neuroinflammation and cognitive deficits, providing insights into potential therapeutic targets for CNS infections.

overall_design: To study the effect of CCR2, we infected CD8a-Cre- and CD8a-Cre+ CCR2 floxed mice with WNV-NS5-E218A intracranially. We isolated corteces and hippocampi at 30 days post infection. Brain tissues were processed into single cells suspension and RNA was extracted for sequencing.

first: Ai

last: Shenjian

first: Klein

last: Robyn


title: Flotillin-2 dampens T cell antigen-sensitivity and functionality

city: Research Triangle Park

first: Michael

last: Fessler

state: NC

address: 111 T.W. Alexander Drive

institute: National Institute of Environmental Health Sciences/NIH

summary: T cell receptor (TCR) engagement triggers T cell responses, yet how TCR-mediated activation is regulated at the plasma membrane remains unclear. Here, we report that deleting the membrane scaffolding protein Flotillin-2 (Flot2) increases T cell antigen sensitivity, resulting in enhanced TCR signaling and effector function to weak TCR stimulation. T cell-specific Flot2-deficient mice exhibited reduced tumor growth and enhanced immunity to infection. Flot2-null CD4+ T cells exhibited increased T helper 1 polarization, proliferation, Nur77 induction, and phosphorylation of ZAP70 and LCK upon weak TCR stimulation, indicating a sensitized TCR-triggering threshold. Single cell-RNA sequencing suggested that Flot2-null CD4+ T cells follow a similar route of activation as wild-type CD4+ T cells but exhibit higher occupancy of a discrete activation state under weak TCR stimulation. Given prior reports that TCR clustering influences sensitivity of T cells to stimuli, we evaluated TCR distribution with super-resolution microscopy. Flot2 ablation increased the number of surface TCR nanoclusters on naïve CD4+ T cells.  Collectively, we posit that Flot2 modulates T cell functionality to weak TCR stimulation, at least in part, by regulating surface TCR clustering. Our findings have implications for improving T cell reactivity in diseases with poor antigenicity, such as cancer and chronic infections.

overall_design: scRNA-seq was performed on Flot2WT or Flot2CD4 naive CD4+ T cells following a 3 hour stimulation with varying concentrations (0, 0.25, or 1 μg/ml) of plate-bound anti-CD3. A fixed dose of soluble anti-CD28 (1 μg/ml) was provided under the conditions of 0.25 or 1 μg/ml of plate-bound anti-CD3. Cells stimulated with 0, 0.25, or 1 μg/ml of plate-bound anti-CD3 were hash-tagged with barcode sequence 'ACCCACCAGTAAGAC', 'GGTCGAGAGCATTCA', or 'CTTGCCGCATGTCAT', respectively, and then combined.

first: Peer

middle: W

last: Karmaus

first: Sookjin

last: Moon


title: CCR2 limits inflammatory functions of CD8 TRM cells that impair recognition memory during recovery from WNV encephalitis

summary: Central nervous system (CNS) resident memory CD8 T cells (TRM) that express IFN-γ have been shown to contribute to neurodegenerative processes, including synapse loss, causing memory impairment. Here, we show that CCR2 deficiency in CD8 TRM that persists within the hippocampus after recovery from CNS infection with West Nile virus (WNV) significantly contributes to poor cognitive outcomes. Using CCR2-deficient mice, we determined that CCR2 expression is not essential for CNS T cell recruitment or virologic control during acute WNV infection. However, transcriptomic analyses of forebrain CCR2+ versus CCR2- CD8 TRM during WNV recovery reveal that CCR2 expression significantly regulates hippocampal CD8 TRM phenotype and function, with increased expression of CD103, granzyme A and IFN-γ. Consistent with this, WNV-recovered Cd8acreCcr2fl/fl mice exhibit decreased recognition memory. Our findings highlight CCR2's role in regulating CD8 T cell-mediated neuroinflammation and cognitive deficits, providing insights into potential therapeutic targets for CNS infections.

overall_design: To study the effect of CCR2, we infected WT and CCR2 KO mice with WNV-NS5-E218A intracranially. We isolated CD8 T cells from corteces and hippocampi at 30 days post infection and extracted RNA for sequencing.

first: Shenjian

last: Ai


title: CCR2 limits inflammatory functions of CD8 TRM cells that impair recognition memory during recovery from WNV encephalitis [RNA-seq]

overall_design: To study the effect of CCR2, we infected CD8a-Cre- and CD8a-Cre+ CCR2 floxed mice with WNV-NS5-E218A intracranially. We isolated corteces and hippocampi at 30 days post infection and extracted RNA for sequencing.


title: High-throughput gene expression analysis with TempO-LINC sensitively resolves complex brain, lung and kidney heterogeneity at single-cell resolution

city: Carlsbad

first: Dennis

last: Eastburn

state: CA

address: 5928 Pascal Court, Suite 100

institute: BioSpyder Technologies, Inc

summary: These datasets are associated with the application of a novel genomics platform, TempO-LINC, for conducting high-throughput transcriptomic analysis on single cells and nuclei. The approach is fundamentally different than almost all other single-cell transcriptome profiling methods in that it does not rely on reverse transcription of mRNA. Instead, TempO-LINC is a novel combination of sensitive oligonucleotide ligation-based chemistry and highly scalable combinatorial barcoding. In this study, we applied TempO-LINC to profile the transcriptomes of multiple sample types. The data demonstrated the ability to identify and annotate at least 50 unique cell populations and positively correlate expression of cell type-specific molecular markers within them. TempO-LINC is a robust new single-cell technology that is ideal for large-scale applications/studies with high data quality.

overall_design: We chose to investigate complex mouse brain cortex, lung and kidney tissues to demonstrate the ability of TempO-LINC to accurately profile and identify a variety of tissue-specific cell types. To demonstrate the performance of TempO-LINC on single nuclei, a challenging sample type that is frequently used for single-cell studies, we used nuclei isolated from each of the mouse tissues for subsequent barcoding with the TempO-LINC workflow.

first: Kevin

last: White

first: Nathan

last: Jayne

first: Salvatore

last: Camiolo

first: Gioele

last: Montis

first: Seungeun

last: Ha

first: Kendall

last: Watson

first: Joanne

last: Yeakley

first: Joel

last: McComb

first: Bruce

last: Seligmann


title: Association of smoking with neurocognition, inflammatory and myeloid cell activation profiles in people with HIV on ART

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Objective: People with HIV (PWH) experience excess comorbidities, including neurocognitive disorders, which are linked to inflammation, particularly monocyte-macrophage activation. Smoking contributes to morbidity and mortality in well-treated PWH. We investigated associations between smoking, neurocognitive function, and inflammation in PWH on ART. Design: We used baseline data on cognition and inflammation from a randomized treatment study among smoking and non-smoking PWH. Participants completed 4 neurocognitive tests (7 measures), with a composite score as the primary measure. Inflammatory markers were plasma sCD14, sCD163, and CCL2/MCP-1; %CD14+ monocytes expressing CD16, CD163, and CCR2; and %CD8+ T cells co-expressing CD38/HLA-DR. Exploratory analyses included a plasma cytokine/chemokine panel, hsCRP, neurofilament light chain (NFL) and monocyte transcriptomes by RNAseq.                                                                                Results: We recruited 58 PWH (26 smokers, 32 non-smokers). Mean composite and individual neurocognitive scores did not differ significantly by smoking status except for the color shape task; smokers exhibited worse cognitive flexibility, with adjusted mean times 317.2 (95%CI 1.4, 632.9) msec longer than non-smokers.  Smokers had higher plasma sCD14 than non-smokers (median(IQR) 1820(1678, 2105) versus 1551(1284, 1760) ng/ml, p=0.009). Other inflammatory markers were not significantly different between smokers and non-smokers. Monocyte transcriptomes showed several functions, regulators and gene sets that differed by smoking status.                                                                                Conclusions: sCD14, a marker of monocyte activation, is elevated in PWH who smoke. While neurocognitive measures and other inflammatory markers did not generally differ, these data implicate smoking-related myeloid activation and monocyte gene dysregulation in the HIV/smoking synergy driving HIV-associated comorbidities.

overall_design: Gene expression profiling by RNA sequencing of monocytes from HIV+/ART smokers and non-smokers

first: Anjana

last: Yadav

first: Ronald

middle: G

last: Collman


title: IL27 as a Novel Biomarker for Pruritus Specific in Nodular Prurigo and Bullous Pemphigoid

city: Wuhan

first: Yifei

last: Wang

address: Baofeng street

institute: Huazhong University of Science and Technology

summary: To uncover shared immune regulatory networks and potential pruritus mechanisms between BP and PN, and provide better treatment strategies for BP and PN.

overall_design: We collected 23 peripheral blood mononuclear cell samples from BP and PN patients, as well as healthy controls, and conducted RNA-seq sequencing analysis.

first: Xin

last: Zhang

first: Chen

last: Shen


title: Crosstalk between cancer-associated fibroblasts and non-neuroendocrine tumor cells in small cell lung cancer involves in glycolysis and antigen-presenting features

city: Changchun

first: Yuanhua

last: Lu

state: Jilin

address: No.1066, Jinhu Road, Guigu Street

institute: Jilin Cancer Hospital

summary: Small cell lung cancer (SCLC) is a highly fatal malignancy, the complex tumor microenvironment (TME) is a critical factor affecting SCLC progression. Cancer-associated fibroblasts (CAFs) are crucial components of TME, yet their role in SCLC and the underlying mechanisms during their interaction with SCLC cells remain to be determined. In this study, a co-culture system comprising MRC5 fibroblasts and SCLC cell lines was constructed. RNA sequencing (RNA-seq) was performed on co-cultured and separately cultured MRC5 and H196 cells to identify differentially expressed genes (DEGs) and enriched signaling pathways. We obsertved that non-neuroendocrine (non-NE) SCLC-derived CAFs exhibited more abundance and DEGs than NE SCLC-derived CAFs did. Enriched glycolysis-related genes, increased glucose uptake, and upregulated glycolytic signaling proteins were found in non-NE SCLC cells when interaction with MRC5 fibroblasts, confirming CAF-mediated glycolysis promotion. Additionally, non-NE SCLC cell-educated CAFs exhibited features of antigen-presenting CAFs (apCAFs), as indicated by the expression of major histocompatibility complex (MHC) molecules. This study emphasizes the pro-tumor function of CAFs in SCLC by promoting glycolysis and impairing T cell function, providing direction for the development of novel therapeutic approaches targeting CAF in SCLC.

overall_design: We performed RNA-sequcing in co-cultured or separately cultured SCLC cell lines H196 and fibroblast MRC5 using BGISEQ platform

first: Hui

last: Li

first: Peiyan

last: Zhao

first: Ying

last: Cheng


title: Effect of BCAT1 depletion on sensitivity to Etoposide in T-cell acute lymphoblastic leukemia cells

city: Padova

first: Erich

last: Piovan

address: via Gattamelata 64

department: Surgery, Oncology and Gastroenterology

country: Italy

institute: University of Padova

summary: High levels of branched-chain amino acid (BCAA) transaminase 1 (Bcat1) have been associated with adverse prognosis and drug resistance in several cancer types. However, the mechanistic role of Bcat1 in T-cell acute lymphoblastic leukemia (T-ALL) development is ill defined.We determined the effects of BCAT1 depletion on cellular sensitivity to DNA damaging agents (etoposide).

overall_design: To study the effects of BCAT1 depletion on cellular sensitivity to DNA damaging agents (etoposide), we performed gene expression profiling by mRNA-seq in CCRF-CEM T-ALL cells depleted of BCAT1 by shRNA. CCRF-CEM cells were transduced with control or two BCAT1-targeting shRNAs (#223, #329) and treated with etoposide (1uM) or vehicle (DMSO) for 24h.

first: Piovan

last: Erich

first: Tosello

last: Valeria

first: DiMartino

last: Ludovica


title: Pharmacological inactivation of a non-canonical gp130 signaling arm attenuates chronic systemic inflammation and multimorbidity induced by a high-fat diet

city: Los Angeles

first: Denis

last: Evseenko

address: 1450 Biggy St

department: Orthopaedic Surgery

institute: University of Southern  California

summary: Interleukin-6 (IL-6) is a major pro-inflammatory cytokine that demonstrates a robust correlation with age and body mass index (BMI) as part of the senescence-associated secretory phenotype. IL-6 cytokines also play a crucial role in metabolic homeostasis and regenerative processes primarily via the canonical STAT3 pathway. Thus, selective modulation of IL-6 signaling may offer a unique opportunity for therapeutic interventions. Our recent studies identified a novel non-canonical signaling pathway that involves prolonged activation of SRC family of kinases (SFK) by IL-6/gp130, where genetic or pharmacological inhibition of this pathway was protective in several acute injury models. This study was designed to assess the effect of a small molecule (R159) that inhibits the non-canonical signaling in a mouse model of multimorbidity induced by chronic inflammation. Aged mice were fed a high-fat diet (HFD) to exacerbate chronic inflammation and inflammaging-related conditions, and R159 significantly decreased systemic inflammatory responses in adipose tissue and liver. R159 was protective against trabecular bone and articular cartilage loss and markedly prevented neurogenesis decline. Moreover, R159 reduced weight gain induced by HFD and increased physical activity levels. These findings suggest that selective pharmacological inhibition of SFK signaling downstream of IL6/gp130 offers a promising strategy to alleviate systemic chronic inflammation and relevant multimorbidity.

overall_design: mRNA sequencing for C57BL/6 mice on high-fat diet and administered R159 or vehicle (Veh)

first: Arijita

last: Sarkar


title: Topical lubrication restores dry eye corneal stroma by producing  reparative  keratocytesacripep promotes corneal regeneration in autoimmune mediated dry eye disease.

city: San Francisco

first: Sarah

last: Knox

state: California

address: 513 Parnassus Ave

department: Cell Tissue Biology

institute: University of California San Francisco

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

overall_design: Refer to individual Series


title: Topical lubrication restores dry eye corneal stroma by producing  reparative  keratocytesacripep promotes corneal regeneration in autoimmune mediated dry eye disease (snRNA-Seq).

summary: Topical lubrication is the most common remedy for relieving the signs and symptoms of dry eye. However, the therapeutic value of lubricating the ocular surface remains relatively unknown. Here we reveal the restorative properties of the simplest form of lubrication in a mouse model of autoimmune-mediated dry eye. We show topical treatment with PBS rescues corneal stromal architecture through restoring the basement membrane and collagen fiber alignment essential for maintaining corneal transparency. At the single cell level we show keratocytes exhibit significant plasticity under chronic injury, with continuous transition from a homeostatic to inflammatory state, and that lubrication converts these inflammatory cells to a unique reparative phenotype. We further identify IL1b-IL1R1-MAPK signaling as a key pathway driving keratocyte inflammation, and that disruption of the IL1b autocrine amplification loop by lubrication is sufficient to reprogram the inflammatory keratocytes towards the reparative state. Thus, our study underscores the regenerative potential of topical lubrication in dry eye, and reveals fibroblast-targeted therapies as a novel approach to restoring ocular surface health.

overall_design: Comparative analysis of gene expression between wilt type, untreated Aire KO (dry eye disease) , Aire KO treated with PBS, and Aire KO treated with 4uM lacripep whole corneas at day 7 of treatment (6 wk of age).

first: Yael

last: Efraim

first: Feeling

last: Yu

first: Ting

last: Chen

first: Dylan

last: Pham

first: Vahid

last: Niknezhad

first: Ka

middle: N

last: Cheong

first: Luye

last: An

first: Hanan

last: Sinada

first: Nancy

middle: A

last: McNamara


title: Topical lubrication restores dry eye corneal stroma by producing  reparative  keratocytesacripep promotes corneal regeneration in autoimmune mediated dry eye disease (Bulk RNA-Seq).


title: Single-nucleus transcriptomic profiling of the diaphragm during mechanical ventilation

city: Changzhi City

first: Dong

last: Zhang

address: 110 South Yan'an Road, Luzhou District

institute: Department of Critical Care Medicine, Heping Hospital Affiliated to Changzhi Medical College

summary: Mechanical ventilation contributes to diaphragm atrophy and muscle weakness, which is referred to as ventilator-induced diaphragmatic dysfunction (VIDD).Through snRNA seq, we demonstrated that diaphragm fibrosis resulting from FAP proliferation, EMT, immune cell infiltration, and diaphragm atrophy which are induced by phrenic nerve ending loss are the underlying causes of VIDD.

overall_design: Four samples are from diaphragm tissue of Japanese white rabbits with large ears

first: Lei

last: Li

first: Yu

last: Wang

first: Yaqian

first: Feng

last: Jiang

first: Wenyan

last: Hao


title: Identification of ALEKSIN as a novel multi-IRF inhibitor of IRF- and STAT-mediated transcription in vascular inflammation and atherosclerosis [HMEC]

city: Poznan

first: Hans

last: Bluyssen

address: Uniwersytetu Poznańskiego 6

department: Laboratory of Human Molecular Genetics

country: Poland

institute: Adam Mickiewicz University

summary: Cardiovascular diseases (CVDs) include atherosclerosis, which is an inflammatory disease of large and medium vessels that leads to atherosclerotic plaque formation. Key factors contributing to onset and progression of atherosclerosis include the pro-inflammatory cytokines Interferon (IFN)α and IFNγ and the Pattern Recognition Receptor (PRR) Toll-like receptor 4 (TLR4). Together, they trigger activation of IFN Regulatory Factors (IRFs) as well as Signal Transducer and Activator of Transcription (STAT)s. Based on their promoting role in atherosclerosis, we hypothesized that combined inhibition of IRFs and STATs blocks pro-inflammatory target gene expression and may be a promising strategy to treat CVDs.  Using comparative in silico docking of multiple IRF-DBD models on a multi-million natural compound library, we identified the novel multi-IRF inhibitor, ALEKSIN. This compound targets the DBD domain of IRF1, IRF2, and IRF8 with the same affinity and simultaneously inhibits expression of multiple IRF-target genes in HMECs in response to IFNa and IFNg. Under the same conditions, ALEKSIN was also shown to inhibit phosphorylation of STATs, potentially through low-affinity STAT-SH2 binding, however  with lower potency as the known multi-STAT inhibitor STATTIC. This was in line with the common inhibition of ALEKSIN and STATTIC observed on genome-wide expression of pro-inflammatory IRF/STAT/NF-κB target genes, as well as on migration of HMECs. Finally, we identified a novel signature of 46 ALEKSIN and STATTIC commonly inhibited pro-atherogenic target genes, that was upregulated in atherosclerotic plaques in aorta's of high-fat diet fed APOE-/- mice and associated with inflammation, proliferation, adhesion, chemotaxis and response to lipid.  Together, this suggests that ALEKSIN represents a novel class of multi-IRF inhibitors, which inhibit IRF- , STAT- and NF-κB-mediated transcription and could offer great promise for the treatment of CVDs. Also, the ALEKSIN and STATTIC commonly inhibited pro-inflammatory gene signature could serve to monitor plaque progression during experimental atherosclerosis.

overall_design: Gene expression profiling by high throughput sequencing in HMEC cell line after tretment with ALEKSIN and STATTIC, inhibitors of IRF- and STAT-mediated transcription


title: A rare non-coding enhancer variant in SCN5A contributes to the high prevalence of Brugada syndrome in Thailand

city: Amsterdam

first: Connie

last: Bezzina

address: Meibergdreef 9

department: Exp. Card.

country: Netherlands

institute: Amsterdam UMC

summary: Brugada syndrome (BrS) is a cardiac arrhythmia disorder that causes sudden death in young adults. Rare genetic variants in the SCN5A gene, encoding the Nav1.5 sodium channel, and common non-coding variants at this locus, are robustly associated with the condition. BrS is particularly prevalent in Southeast Asia but the underlying ancestry-specific factors remain largely unknown. Methods: Genome sequencing of BrS probands and population-matched controls from Thailand was performed to identify rare non-coding variants at the SCN5A-SCN10A locus that were enriched in BrS cases. A likely causal variant was prioritised by computational methods and introduced into human pluripotent stem cell (hiPSC) lines using CRISPR-Cas9. The effect of the variant on SCN5A expression and Nav1.5 sodium channel current was then assessed in hiPSC-derived cardiomyocytes (hiPSC-CMs). Results: A rare non-coding variant in an SCN5A intronic enhancer region was highly enriched in BrS cases (detected in 3.9% of cases with a case-control odds ratio of 45.2). The variant affects a nucleotide conserved across all mammalian species and predicted to disrupt a Mef2 transcription factor binding site. Heterozygous introduction of the enhancer variant in hiPSC-CMs caused significantly reduced SCN5A expression from the variant-containing allele and a 30% reduction in Nav1.5-mediated sodium current density compared to isogenic controls, confirming its pathogenicity. Patients with the variant had severe phenotypes, with 89% experiencing cardiac arrest. Conclusions: This is the first example of a functionally validated rare non-coding variant at the SCN5A locus and highlights how genome sequencing in understudied populations can identify novel disease mechanisms. The variant partly explains the increased prevalence of BrS in this region and enables the identification of at-risk variant carriers to reduce the burden of sudden cardiac death in Thailand.

overall_design:
The RE5 GRCh38:chr3-38580380-A-C variant was introduced in heterozygous state in the PGP1 hiPSC line by CRISPR/Cas9-mediated editing (Synthego).
In order to quantify the potential cis-regulatory effect of the RE5 variant ( intronic) on SCN5A allelic expression we isolated bulk messanger RNA from cardiomyocytes of the control PGP1-SV1 hiPSC line and isogenic variant-carrying A7 hiPSC line, followed by RNAseq analysis for quantification of the allele-specific transcript outputs.
To distinguish transcripts originating from the two alleles, since the intronic variant was not identifiable from the messenger RNA, we took advantage of a heterozygous exonic variant (c.3183A>G ) located 596bp from the intronic variant and determined their phase by Sanger sequencing of the genomic fragment.

first: Roddy

last: Walsh

first: John

last: Mauleekoonphairoj

first: Isabella

last: Mengarelli

first: Arie

middle: O

last: Verkerk

first: Karel

last: van Duijvenboden

first: Vincent

last: Christoffels

middle: R


title: Simultaneous treatment of castration-resistant prostate cancer cells with the DNA Demethylating Agent Decitabine and S-adenosylmethionine leads to synergistic anti- cancer effects.

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary: A general problem of methylating and demethylating agents is a lack of limitation to the promotors of tumor suppressor genes or proto-oncogenes respectively. This may cause adverse consequences. Thus, the question was raised if the simultaneous application of DNA-demethylating agents and S-adenosylmethionine could reverse these effects.

overall_design: PC-3 cells were treated simultaneously with Decitabine and S-adenosylmethionine. RNA-Seq was performed.

first: Thomas

last: Schmidt

first: Julio

last: Cordero


title: MuSC dysfunction contributes to dystrophic progression and impaired regeneration in the mdx mouse

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

institute: Ottawa Hospital Research Institute


title: One deficiency, different outcomes: Succinate dehydrogenase loss in chromaffin cell vs. fibroblast models of paraganglioma

city: Rochester

first: Cristina

last: Correia

state: Minnesota

address: Kellen Bld 3 th Floor, 200 1st street SW

institute: Mayo Clinic

summary: Heterozygosity for loss‐of‐function alleles of the genes encoding the four subunits of succinate dehydrogenase (SDHA, SDHB, SDHC, SDHD), as well as the SDHAF2 assembly factor predispose affected individuals to pheochromocytoma and paraganglioma (PPGL), two rare neuroendocrine tumors that arise from neural crest-derived paraganglia. Tumorigenesis results from loss of the remaining functional Sdhx gene copy, leading to a cell with no functional SDH and a defective tricarboxylic acid (TCA) cycle. It is believed that the subsequent accumulation of succinate competitively inhibits multiple dioxygenase enzymes that normally suppress hypoxic signaling and demethylate histones and DNA, ultimately leading to increased expression of genes involved in angiogenesis and cell proliferation. Why SDH loss is selectively tumorigenic in neuroendocrine cells remains poorly understood. Here we characterize two available murine SDH-loss cell lines, one representing PPGL-susceptible chromaffin cells and the other PPGL-resistant fibroblasts. Consistent with previous analyses, we find strikingly different effects of SDH loss in these two cellular contexts, including evidence of residual Complex I activity only in SDH-loss immortalized mouse chromaffin cells. This work supports the hypothesis that chromaffin cells may uniquely tolerate SDH loss and sets the stage for analyses of unique vulnerabilities in SDH-loss chromaffin cells.

overall_design: RNAseq data of 12 samples: immortalized mouse chromaffin cells (imCC) (DOI:10.1016/j.ccr.2013.04.018) parental (WT) or SDHB-loss (n=6) in three independent experiments and immortalized mouse embryonic fibroblasts (iMEF) (DOI:10.18632/oncotarget.23639) parental (WT) or and SDHC-loss (n=6) in three independent experiments.

first: Jim

last: Maher

first: Fatimah

last: Al Khazal

first: Judith

last: Favier


title: TEFM facilitates uterine corpus endometrial carcinoma progression by activating ROS-NFκB pathway

city: Kaifeng

first: Dengke

last: Bao

state: Henan

address: Jinming Road

department: School of Pharmacy

institute: Henan University

summary: Background: Mitochondrial transcription elongation factor (TEFM) is a recently discovered factor involved in mitochondrial DNA replication and transcription. Previous study has reported that abnormal expression of TEFM can disrupt the assembly of mitochondrial respiratory chain and thus mitochondrial function. However, the role of TEFM on Uterine corpus endometrial carcinoma (UCEC) progression remains unclear. The present study aims to investigate the expression of TEFM in tumor tissue of UCEC and the effect of abnormal TEFM expression on malignant phenotype of UCEC cells. Methods: The expressions of TEFM were measured in tumor tissues and cell lines of UCEC by immunohistochemistry, Western blotting, and real-time quantitative PCR assays. Besides, the effects of TEFM knockdown or overexpression on UCEC cell growth, metastasis, apoptosis, and autophagy were also determined using EdU, colony formation, flow cytometry, TUNEL, transmission electron microscopy assays. Xenograft model was used to confirm the role of TEFM on proliferative potential of UECE cells in vivo. Results: Our bioinformatics analysis of CPTAC data showed that TEFM is abnormally overexpressed in UCEC and its upregulation was significantly associated with poor survival of patients with UCEC. We found that TEFM upregulation significantly promoted the growth and metastasis of UCEC cells. Mechanically, TEFM upregulation impaired the function of mitochondria, decreased their membrane potential and activated the AKT-NFκB pathway by promoting reactive oxygen species (ROS) production, leading to enhanced intracellular autophagy and thus UCEC growth and metastasis.  Conclusion: This study demonstrates that TEFM positively regulates autophagy to promote the growth and metastasis of UCEC cells, which provides potential prognostic biomarker and therapeutic target for the treatment of UCEC.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Ishikawa cells and its TEFM gene overexpression derivatives (TEFM-Ishikawa).Three independent biological replicates were prepared for RNA isolation and RNA sequencing.

first: Ruixia

last: Guo

first: Jia

last: Lei

first: Qingguo

last: Zhu


title: Bone morphogenetic protein increases tau phosphorylation and secretion in tauopathies in an APOE dependent manner

city: Chicago

first: Amira

last: Affaneh

state: IL

address: 303 E. Chicago, Ward 10-233

institute: Northwestern University

summary: To investigate the contribution of APOE genotype on neuronal transcription of key Alzheimer and BMP-relevant genes

overall_design: Neuronal cells were differentiated from two different IPSC lines and  isogenic controls (4 lines total) using the NGN2 viral protocol. Cells were grown for 35 days to ensure maturity prior to collection for RNA-seq

first: Anne

last: Linden

first: Chian-Yu

last: Peng


title: Amyloid-β increases MBP and MOBP translation in oligodendrocytes through dysregulation of hnRNP A2-dependent RNA dynamics

city: Leioa

first: Fernando

last: García-Moreno

state: Bizkaia

address: Barrio Sarriena s/n Edificio Sede

country: Spain

institute: Achucarro BCN

summary: Oligodendrocyte dysfunction, myelin degeneration, and white matter structural alterations are critical events in Alzheimer's disease (AD) that contribute to cognitive decline. A key hallmark of AD, Aβ oligomers, disrupt oligodendrocyte and myelin homeostasis, but a comprehensive global analysis of the mechanisms involved is lacking. Here, transcriptomic profiling of Aβ-exposed oligodendrocytes revealed widespread gene expression changes, particularly affecting pathways related to RNA localisation. Among the genes identified, we focused on Hnrnpa2/b1, the gene encoding the hnRNP A2 protein, which is essential for RNA transport and translation of myelin proteins. We confirmed aberrant upregulation of hnRNP A2 in hippocampal oligodendrocytes from post-mortem human brains of early-stage AD patients, Aβ-injected mouse hippocampi and Aβ-treated disrupting cells in vitro. RIP-seq analysis of the hnRNP A2 interactome revealed attenuated interactions with Hnrnpk and Hnrnpa2/b1, while interactions with Mbp and Mobp were enriched, suggesting changes in RNA metabolism of molecules associated with mRNA transport of myelin proteins. Aβ increased the total number and dynamics of mRNA-containing granules, facilitating local translation of the myelin proteins MBP and MOBP and attenuating Ca2+ signalling. These findings suggest that Aβ oligomers disrupt RNA metabolism mechanisms crucial for oligodendrocyte myelination through dysregulation of hnRNP A2 and myelin protein levels, potentially affecting oligodendroglia Ca2+ homeostasis.

overall_design: For, the hnRNP A2 interactome analysis, total RNA from three biological replicates of hnRNP A2 and IgG IPs, as well as three replicates of input mRNA.

first: Adhara

last: Garminde-Blasco

first: Rodrigo

last: Senovilla-Ganzo

first: Uxue

last: Balantzategi

first: Carlos

last: Matute

first: Jimena

last: Baleriola

first: Elena

last: Alberdi


title: MuSC dysfunction contributes to dystrophic progression and impaired regeneration in the mdx mouse [scRNA-seq]

first: Theodore

last: Perkins

summary: Duchenne muscular dystrophy (DMD) is a devastating disease characterized by progressive muscle wasting and limitation of life. In addition to the inherent weakness of dystrophin-deficient muscle, the dysfunction of resident muscle stem cells significantly contributes to disease progression. Using the mdx mouse model of DMD, we performed an in-depth characterization of disease progression and muscle stem cell (MuSC) function in dystrophin deficient skeletal muscle using immunohistology, isometric force measurements, transplantation assays, and transcriptomic analysis. Here, we performed single cell RNA-sequencing of wild-type (WT) and mdx myogenic cells before and 5-days following cardiotoxin injury.

overall_design:
Muscle stem cells from uninjured and 5 days post cardiotoxin-injured WT and mdx Myf5creER;ROSA-mTmG mice were FACS-isolated.

Two processed data files on the Series were reanalyzed with a different version of Cell ranger and reference for this study. The files are from GSM7498324 and GSM7498326 of GSE235284.

first: Marie

middle: E

last: Esper

first: Caroline

last: Brun

first: Alexander

middle: Y

last: Lin

first: Peter

last: Feige

last: Catenacci

first: Marie-Claude

last: Sincennes

first: Morten

last: Ritso

first: Michael

last: Rudnicki


title: MuSC dysfunction contributes to dystrophic progression and impaired regeneration in the mdx mouse [bulk RNA-seq]

summary: Duchenne muscular dystrophy (DMD) is a devastating disease characterized by progressive muscle wasting and limitation of life. In addition to the inherent weakness of dystrophin-deficient muscle, the dysfunction of resident muscle stem cells significantly contributes to disease progression. Using the mdx mouse model of DMD, we performed an in-depth characterization of disease progression and muscle stem cell (MuSC) function in dystrophin deficient skeletal muscle using immunohistology, isometric force measurements, transplantation assays, and transcriptomic analysis. Here, we performed bulk RNA-sequencing of wild-type (WT) and mdx myogenic cells in different conditions.

overall_design: Bulk RNA-sequencing of mogenic cells derived from WT and mdx Pax7-nGFP mice was performed in biological triplicate for 4 conditions (24 libraries total). PAX7 expressing MuSCs were isolated from hindlimb muscles before and 3-days after cardiotoxin injury. Myoblasts and 2-day differentiated myotubes were also collected after in vitro culture of WT and mdx PAX7 expressing cells.


title: Oxidative stress, altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish

city: LONDON

first: Mariya

last: Moosajee

address: 1 Midland Rd

country: United Kingdom

institute: The Francis Crick Institute

summary: Reactive oxygen species (ROS) within the retina play a key role in maintaining function and cell survival. However, excessive ROS can lead to oxidative stress, inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia (CHM), an X-linked chorioretinal dystrophy which predominantly affects the photoreceptors, retinal pigment epithelium (RPE) and choroid. In this study, we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration, upregulation of oxidative, ER stress and apoptosis markers, and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2-NBDG glucose uptake assay, but after overexpression of human PFKM, it partially rescued the retinal phenotype and glucose uptake, but without modifying the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach.

overall_design: Choroideremia (CHM) is a x-linked inherited retinal dystrophy, caused by mutations in the CHM gene. It is a progressive condition leading to  complete blindness. We are working on a chm zebrafish model, which shows a widespread severe degenerative phenotype, with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.

first: Pablo

last: Soro-Barrio

first: Cécile

last: Méjécase


title: Breast cancer cell lines

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus


title: Effect of TDO2/IDO dual inhibitor AT0174 on  human MDA-MB-453 breast cancer cells

summary: To investigate global transcriptomics of human MDA-MB-453 breast cancer cells in response to the TDO2/IDO dual inhibitor AT0174 treatment in compared with the vehicle control

overall_design: Breast cancer cell line MDA-MB-453 at attached culture and forced suspension culture was treated with AT0174 or vehicle control (DMSO) for 48 hours, the cells were then collected for Bulk RNA sequencing. All conditions were performed with biological triplcates.

first: Li-Wei

last: Kuo

first: Lyndsey

last: Crump

first: Kathleen

middle: I

last: O'Neil

first: Michelle

last: Williams

first: Jessica

middle: L

last: Christenson

first: Nicole

last: Spoelstra

first: Jennifer

middle: K

last: Richer

first: Meher

middle: P

last: Boorgula


title: Global transcriptomics analysis for TDO2 alteration in human triple-negative breast cancer cell lines

summary: To elucidate the downstream transcriptomics changes in reponse to TDO2 alteration including shRNA knockdown, overexpression and TDO2/IDO duak inhibitor treatments in human triple-negative breast cancer cell lines.

overall_design: Each condition with biological triplicates. Human triple-negative breast cancer cell line BT549 with TDO2 overexpression (OE) in compared with control empty vector (EV); BT549 with shRNA TDO2 knockdown (shTDO2-082 or shTDO2-098) vs. shNegative control (shNeg);  BT549 at forced suspension culture treated with TDO2/IDO dual inhibitor AT0174 for 48 hours ; SUM159PT at forced suspension culture treated with TDO2/IDO dual inhibitor AT0174 for 48 hours


title: DOG1 role in BRM SWI/SNF complex mediated control of seed quality and physiology

city: Warsaw

first: Michal

last: Krzyszton

address: Pawinskiego 5a

institute: Institute of Biochemistry and Biophysics, Polish Academy of Sciences

summary: The SWI/SNF chromatin remodeling complex is involved in various aspects of plant development and stress responses. In this study, we investigated the role of BRM, a core subunit of the SWI/SNF complex, in seed physiological quality in Arabidopsis thaliana. We found that brm-3 seeds exhibited enlarged size, reduced yield, increased longevity, and enhanced secondary dormancy, but no change in primary dormancy or salt tolerance. We also showed that some of these phenotypes were dependent on DOG1, a key regulator of seed dormancy, as they were reversed in the brm-3xdog1-4 double mutant. Transcriptomic and metabolomic analyses revealed that BRM and DOG1 synergisticly modulate the expression of majority genes and metabolites. In contrast some of the transcriptomic and metabolomic changes including glutathione were depended on DOG1. Moreover, we demonstrated that BRM controls secondary dormancy directly through DOG1 by binding to and remodeling its 3’ region, where an antisense promoter of DOG1 is located. Our results suggest that BRM and DOG1 cooperate to control seed physiological quality by fine-tuning the chromatin state and metabolic status of seeds. This study provides new insights into the molecular mechanisms of seed dormancy and longevity, and the interplay between chromatin remodelling at DOG1 locus.

overall_design: Comparison of Col-0, dog1-4, brm-3 and double brm-3 x dog1-4 mutants dry seed transcriptomes (four biological replicas).

first: Ruslan

last: Yatusevich

first: Magdalena

last: Wrona

first: Julia

last: Zinsmeister

first: Szymon

last: Swiezewski


title: Transcriptomic Analysis of the Candida albicans Response to Treatment with Baicalin

city: Hefei

first: Wenqian

last: Li

address: Longzihu Road

institute: Anhui University of Chinese Medicine

summary: In order to investigate differential gene expression at high resolution, here, we have performed RNA sequencing analysis of samples obtained from Candida albicans cells grown in the presence or absence of baicalin. Overall treatment with baicalin resulted in 496 up-regulated and 346 down-regulated genes.

overall_design: Candida albicans strain SC5314 was grown in YPD medium overnight, washed with PBS and cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum at 2.5×10^4 CFU/mL and incubated at 37 ℃ for 24 hours in the presence or absence of baicalin at 500 μg/mL. Total RNA was extracted and mRNA enriched by magnetic beads with oligo(dT). The mRNA was randomly broken by adding fragmentation buffer. Short fragments of double-stranded cDNA generated by reverse transcription were subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase for 15 PCR cycles. After quantified by Qubit 4.0, paired-end RNA-seq sequencing library was sequenced with the NovaSeq 6000 sequencer (2 × 150 bp read length). Three biological replicates were obtained for each condition (treated and untreated).

first: Yiyuan

last: Pan

first: Kelong

last: Ma


title: An Efficient and Cost-Effective Approach to Generate Functional Human Inducible Pluripotent Stem Cell-Derived Astrocytes

first: Tanner

last: Shull

address: 1735 W Harrison St

department: Microbial Pathogens and Immunity

institute: Rush University Medical Center

summary: Human inducible pluripotent stem cell (hiPSC)-derived astrocytes (iAs) are critical to study astrocytes in health and disease. They provide several advantages over human fetal astrocytes in research, which include consistency, availability, disease modeling, customization, and ethical considerations. The generation of iAs is hampered by the requirement of Matrigel matrix coating for survival and proliferation. We provide a protocol demonstrating that human iAs cultured in the absence of Matrigel are viable and proliferative. Further, through a side-by-side comparison of cultures with and without Matrigel, we show significant similarities in astrocyte-specific profiling, including morphology (shape and structure), phenotype (cell-specific markers), genotype (transcriptional expression), metabolic (respiration), and functional aspects (glutamate uptake and cytokine response). In addition, we report that, unlike other CNS cell types, such as neuronal progenitor cells and neurons, iAs can withstand the absence of Matrigel coating. Our study demonstrates that Matrigel is dispensable for the culture of human iPSC-derived astrocytes, facilitating an easy, streamlined, and cost-effective method of generating these cells.

overall_design: Astrocyte derived induced pluripotent stem cells were subjected to organic coating matrix (control) or no matrix (experimental) with n=2 for control and n=4 for experimental, with 2 different cell lines used within experimental


title: ALTERED MERISTEM PROGRAM1 impairs RNA silencing through repressing the biogenesis of inverted repeats-derived siRNAs in Arabidopsis [small RNA-seq]

city: Riverside

first: Ye

last: Xu

address: 900 University Ave

institute: University of California, Riverside

type: Non-coding RNA profiling by high throughput sequencing

summary: We profiled the small RNA of SUCSUL, SUCSUL amp1lamp1 and Col in Arabidopsis to study the role of AMP1 in siRNA-mediated gene regulation

overall_design: small RNA-seq to examine the total small RNA profile in Arabidopsis SUCSUL and SUCSUL amp1lamp1 transgenic lines.

first: Brandon

last: Le

first: Lin

last: Liu

first: Xuemei

last: Chen


title: Blood analysis reveals differences in innate inflammatory sensitivity between species

city: Cambridge

first: wenzhong

last: xiao

state: ma

address: 38 sidney st, suite 161

institute: massachusetts general hospital

summary: Vertebrates differ greatly in responses to pro-inflammatory agonists such as bacterial lipopolysaccharide (LPS), complicating use of animal models to study human sepsis or inflammatory disorders.  We compared transcriptomes of resting and LPS-exposed blood from rabbit, pig, sheep, cow, chimpanzee, human, mice, rats, baboon, and rhesus.

sample_organism:
Macaca
Papio anubis
Pan troglodytes
Homo sapiens
Sus scrofa
Bos taurus
Ovis aries
Oryctolagus cuniculus
Mus musculus
Rattus norvegicus

first: David

middle: J

last: Gregory

first: Feifei

last: Han

first: Wenzhong

last: Xiao

first: H

last: Warren


title: ALTERED MERISTEM PROGRAM1 impairs RNA silencing through repressing the biogenesis of inverted repeats-derived siRNAs in Arabidopsis [Methyl-seq]

summary: We examed the methylation level of SUCSUL, SUCSUL amp1lamp1 and Col in Arabidopsis to study the role of AMP1 in siRNA-mediated gene regulation

overall_design: Methyl-seq to examine the methylation profile of Arabidopsis SUCSUL and SUCSUL amp1lamp1 transgenic lines.


title: ALTERED MERISTEM PROGRAM1 impairs RNA silencing through repressing the biogenesis of inverted repeats-derived siRNAs in Arabidopsis

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

overall_design: Refer to individual Series


title: TBX21 attenuates colorectal cancer progression via a ARHGAP29/RSK/GSK3β dependent manner

city: Jining

first: Wenzhi

last: Shen

address: No. 133 Hehua Road

institute: Jining Medical University

summary: To investigate the function and mechanism of TBX21 in colorectal cancer, we established RKO overexpressed TBX21 gene stable cell lines by using levti-virus system.

overall_design:
We then performed gene expression profiling analysis using data obtained from RNA-seq of RKO-OECtrl and RKO-OETBX21 cells.
Comparative gene expression profiling analysis of RNA-seq data for RKO-OECtrl and RKO-OETBX21 cells.

first: Xinyu

last: Jiang

first: Yongming

last: Huang


title: Single-cell RNA-seq data of human PBMC from amyotrophic lateral sclerosis patients

city: FUJISAWA

first: Yuumi

last: Okuzono

state: KANAGAWA

address: 26-Muraoka-higashi 2-chome

country: Japan

institute: Takeda Pharmaceutical Company Limited

summary:
Importance: Amyotrophic lateral sclerosis demonstrated changes in peripheral immune cells and proteins. However, the relationship between comprehensive immune profiles and clinical progression remained unclear.
Objective: To identify the immune cells and proteins related to amyotrophic lateral sclerosis progression rate.
Design: This case-control study enrolled healthy volunteers and patients with amyotrophic lateral sclerosis from March 29, 2021, to October 31, 2022.
Setting: Tokushima University Hospital and Takeda Pharmaceutical Company Limited in Japan.
Participants: This study screened 46 subjects to enroll 30 patients with amyotrophic lateral sclerosis within 2 years from onset and 10 healthy volunteers. Patients with rapid and non-rapid amyotrophic lateral sclerosis were those with Revised Amyotrophic Lateral Sclerosis Functional Rating Scale decreases of ≥1.0/month and <1.0/month, respectively.
Exposure(s): Peripheral blood samples were collected.
Main Outcome(s) and Measure(s): The progression rate as assessed with the Revised Amyotrophic Lateral Sclerosis Functional Rating Scale decrease/month and the immune cell and protein profiles via single-cell RNA sequencing and immunoproteomics.
Results: Samples of 7 (mean [standard deviation] age: 69.8 [14.4] years; male, 3) and 23 (60.7 [10.8] years; male, 17) patients with rapid and non-rapid amyotrophic lateral sclerosis, respectively, and 10 healthy volunteers (63.6 [10.2] years; male, 7) were analyzed. The ratios of T helper 17/regulatory T cells, mature/naïve CD8 T cells, and mature/naïve natural killer cells were significantly higher in rapid than in non-rapid amyotrophic lateral sclerosis. The ratio of T helper 17/regulatory T cells was significantly correlated with the progression rate. The immunoproteomics identified killer cell lectin-like receptor D1, trefoil factor 2, keratin 19, interleukin-17A, YTH N6-methyladenosine RNA binding protein F3, and neutrophil cytosolic factor 2 as significantly elevated in rapid amyotrophic lateral sclerosis. Cell type frequency and protein expression, such as T helper 17 cell–interleukin-17A and mature CD8 T cell–killer cell lectin-like receptor D1, were significantly correlated.
Conclusions and Relevance: The progression rate was related to the increase of T helper 17 cells versus regulatory T cells and titers of T helper 17 cell- and CD8 T cell-related immunoproteins in patients with amyotrophic lateral sclerosis. These results provide promising biomarkers and targets for amyotrophic lateral sclerosis disease-modifying therapies.

overall_design: Examination of gene expression profile of human PBMC from amyotrophic lateral sclerosis patients.

first: Tatsuo

last: Ito

first: Koji

last: Fujita

first: Dnyaneshwar

last: Warude

first: Shuuichi

last: Miyakawa

first: Yoshimi

last: Mihara

first: Naoko

last: Matsui

first: Hiroyuki

last: Morino

first: Yusuke

last: Kikukawa

first: Yuishin

last: Izumi


title: HIF-2a in the development of NASH

city: La Jolla

first: Yun Sok

last: Lee

address: 9500 Gilman Dr MC0673

department: Medicine

institute: University of California San Diego

summary: We studied the effect of myeloid HIF-2a on the development of NASH and the underlying mechanisms.

overall_design: WT and myeloid-specific HIF-2a KO mice were fed NASH-inducing high fat high cholesterol diet. Non-paranchymal liver cells were isolated using a collagen fusion method and CD45+ live cells were sorted for scRNA-seq analysis.

first: Yun


title: Knockdown of hsa_circ_0008922 inhibits the progression of glioma

city: Nanning

first: Chunhong

last: Xue

address: 22 Shuangyong Road

department: Department of Histology and Embryology

institute: Guangxi Medical University

summary: Background: we preliminarily outlined the expression of hsa_circ_0008922 in glioma and explored its biological functions. Methods:with RNA sequencing of a panel of glioma tissues and normal brain tissues, The 10 tissues were divided into two groups:C (normal brain tissue, n = 5) and T (tumor tissue, n = 5). With the hsa_circ_0008922 downregulated cells, a series of assays were carried out as follows. Results:We found that the expression of hsa_circ_0008922 in glioma tissues was 3.4 times higher than that in normal tissues. And the expression of has_circ_0008922 was correlated with WHO tumor grade. After down-regulating the expression of hsa_circ_0008922, malignant biological behavior of glioma cells was inhibited, such as cell proliferation, colony formation, migration, and invasion.

first: Chun-Hong

first: Chang

last: Liu