title: The hydrolase receptor DWARF14 is required for zaxinone perception in plants

city: Thuwal

first: Juan Camilo

last: Moreno Beltran

address: King Abdullah University of Science and Technology

country: Saudi Arabia

institute: KAUST

summary: Strigolactones (SLs) are plant hormones involved in plant growth, stress response and plant-organism interactions. DWARF14 (D14) is a α/β hydrolase involved in the perception of SLs in plants. Zaxinone has been reported as a plant endogenous apocarotenoid that modulates growth and biotic interactions, however, the molecular basis of its perception remains elusive. Here we identified a new D14 ligand, the apocarotenoid zaxinone. We showed that hundreds of genes, and specifically CAROTENOID CLEAVAGE DEOXYGENASE7 (CCD7) and CCD8, require At/OsD14, and at lower extent MORE AXILLARY BRANCHING2 (MAX2)/D3, for their transcriptional induction. We find that zaxinone and D14 physically interact in vitro with lower affinity than GR24; the resolution of the AtD14-zaxinone complex, by X-ray crystallography, provided additional evidence that zaxinone antagonizes SL by binding D14. Zaxinone treatments in d14 mutants revealed that At/OsD14 are essential to trigger the induction of CCD7 and CCD8 genes, SL content (roots and exudates) and Striga seed germination validating their interaction in planta. Moreover, OsD14 is required to trigger the zaxinone growth-promoting effect in roots. These findings reveal a perception mechanism for the hormone candidate zaxinone through the SL receptor D14 to regulate transcription of SL genes, SL content and growth in higher plants.

overall_design: To investigate the function of zaxinone on gene expression, we treated 5-weeks old Arabidopsis plants, including wt col-0, d14, kai2 and max2 mutants, by applying this compound in the hydroponic media. Root samples were harvested after 6 hours of treatment.

first: Juan

last: Moreno

first: Umar

last: Hameed

first: Aparna

last: Balakrishna

first: Abdugaffor

last: Ablazov

first: Muhamad

last: Jamil

first: Jianing

last: Mi

first: Kit

middle: X

last: Liew

first: Alexandre

last: de Saint Germain

first: Stefan

last: Arold

first: Salim

last: Al-Babili


title: In vitro and in vivo efficacy of the antimycobacterial molecule SQ109 against the human pathogenic fungus, Cryptococcus neoformans

status: Public on Jun 16 2025

city: Blacksburg

first: Ramu

last: Anandakrishnan

state: VA

address: 1410 Prices Fork Rd., Lab 101

department: Biomedical Sciences

country: USA

institute: Edward Via College of Osteopathic Medici

type: Expression profiling by high throughput sequencing

summary: Cryptococcosis is an opportunistic fungal infection affecting individuals with compromised immunity, particularly those with HIV. The limited accessibility to effective treatments, emerging resistance to current antifungals, and treatment-related toxicities underline the pressing need for more effective therapeutic options. In this study, we conducted a whole-cell screening of ~ 3,700 FDA-approved drugs and clinical molecules against the Cryptococcus neoformans H99 strain to identify potential antifungal candidates. The anti-mycobacterial agent SQ109 was identified as one of the most potent hits, with broad antifungal activity. SQ109 exhibited potent activity against Cryptococcus spp., with an MIC90 of 4 μg/mL. In the time-kill assay, SQ109 demonstrated fungicidal activity against proliferating cryptococcal cells in a concentration-dependent manner. Unlike fluconazole (FLC) and flucytosine (5-FC), C. neoformans showed minimal tendency to develop resistance to SQ109 during frequent passaging. Furthermore, SQ109 exhibited a potent efficiency in the murine model of cryptococcal infection, resulting in a 50% survival rate among the group treated with 25 mg/kg for 10 consecutive days. The transcriptomic analysis revealed that SQ109 disrupts ergosterol biosynthesis, affecting membrane integrity and oxidative stress homeostasis, which aligns with its interaction with other ergosterol pathway inhibitors, including FLC.  Additionally, molecular docking and structural analysis indicated that squalene synthase protein ERG9 is the most likely target of SQ109 within the ergosterol biosynthesis machinery of cryptococcal cells.  These findings highlight the therapeutic potential of SQ109 in combating cryptococcal infections, both as a standalone therapy and as an adjuvant to FLC monotherapy.

overall_design: A total of 18 clinical isolates representing C. neoformans/gattii complex were included in this study. Additional 6 clinical isolates of clinically relevant fungi, including Candida parapsilosis, C. auris, and Aspergillus fumigatus were involved in susceptibility testing. Determination of the MIC for SQ109 and standard antifungals, AmB and FLC, was conducted as described in the Clinical and Laboratory Standards Institute (CLSI) guidelines M27-A3 for yeast and M38-A2 for filamentous fungi.

first: Alkashef

last: Nour

first: Salama

last: Ehab

first: Anandakrishnan

last: Ramu

first: Hazbun

last: Tony

first: Hoernig

last: Micah

first: Brown

last: Anne

first: Lawrence

last: Christopher

first: Saleem

last: Mohamed


title: IL-13 decreases suceptibility to airway epithelial SARS-CoV-2 infection but increases disease severity in vivo [scRNA-seq]

status: Public on Jun 30 2025

city: Iowa city

first: Alejandro

middle: Pezzulo

last: Colmenares

state: Iowa

address: 169 Newton Road

department: Internal medicine

institute: University of Iowa

summary: Human airway epithelia (HAE) undergo inflammation-induced remodeling in chronic lung diseases such as asthma and chronic bronchitis. The role of type 2 inflammation-induced epithelial remodeling in SARS-CoV-2 infection and the course of COVID-19 is unclear, moreover, there is discrepancy in the literature regarding the potential benefit of treatments that modulate type 2 inflammation. We investigated the role of IL-13-induced inflammation on SARS-CoV-2 binding/entry, replication, and host response in primary HAE cells in vitro and in a model of mouse-adapted SARS-CoV-2 in vivo. IL-13 protected airway epithelial cells from SARS-CoV-2 infection in vitro by decreasing the abundance of ACE2- expressing ciliated cells rather than by neutralization in the airway surface liquid or by interferon-mediated antiviral effects. In contrast, IL-13 worsened the severity of disease in mice in vivo; the effects were mediated by eicosanoid signaling and were abolished in mice deficient in the phospholipase A2 enzyme PLA2G2D. We conclude that IL-13-induced inflammation affects multiple steps of SARS-CoV-2-induced disease pathogenesis. Whereas IL-13-induced inflammation may be protective against initial infection at the airway epithelium, it enhances disease severity once infection progresses in vivo; blockade of IL-13 and/or eicosanoid signaling may be protective against progression to severe lung disease.

overall_design: To investigate the role of IL-13 induced inflammation on SARS-CoV-2 in vitro, we treated HAE from 2 donors with 20 ng/mL recombinant IL-13 or 20 ng/mL recombinant IL-17 combined with 10 ng/mL tumor necrosis factor alpha (TNFα) for 4 or 55 days. The cytokines were applied to both apical and basolateral side of HAE. The cells were then infected with SARS-CoV-2 (MOI 0.1), the strain isolated from the first US patient (2019-nCoV/USA-WA1/2020, GenBank:MN985325.1) for 6 or 72 hours.

first: Shreya

last: Ghimire

first: Biyun

last: Xue

first: Kun

last: Li

first: Ryan

middle: M

last: Gannon

first: Christine

middle: L

last: Wolford-Lenane

first: Andrew

last: Thurman

first: Huiyu

last: Gong

first: Grace

middle: C

last: Necker

first: Jian

last: Zheng

first: David

middle: K

last: Meyerholz

first: Stanley

last: Perlman

first: Paul

middle: B

last: McCray

middle: A

last: Pezzulo


title: Bulk RNA sequencing on hepatic tissues from colitis mice treated with a sublethal indirubin dose.

status: Public on Jun 15 2025

city: Hong Kong

first: Yiqi

last: Xu

address: Room 201-207 of 2/F of Building 15W, Phase Three

country: Hong Kong

institute: Centre for Chinese Herbal Medicine Drug Development Limited

summary: Many plant-derived bioactive molecules with low solubility and permeability can cause hepatocyte injury. However, the mechanism by which they induce hepatic damage without passive diffusion into the hepatic circulatory system remains unclear. In this study, we demonstrate that indirubin, the main component of indigo naturalis with poor aqueous solubility, predisposes mice with chronic colitis to hepatic injury.  This closely mimics the hepatic damage commonly observed in ulcerative colitis patients treated with indigo naturalis. To elucidate the mechanism of indirubin-induced hepatocyte injury in chronic colitis, we performed bulk RNA sequencing on hepatic tissues from DSS-induced colitis mice treated with a sublethal indirubin dose.

overall_design: Chronic colitis was induced in C57BL/6J mice using three cycles of dextran sulfate sodium (DSS) administration. Each cycle comprised 1 week of 1.8% (w/v) DSS in drinking water followed by 1 week of recovery. The mice were randomised into 3 groups: (1) the control group received 200 μL of sterile water orally each day; (2) the DSS group received 200μL of sterile water orally each day; (3) the Indirubin groups were given 1g/kg/day of Indirubin in 200μL sterile water orally each day

last: XU

first: Jingchun

last: SHI

first: Heung-Lam

last: MOK

first: Cheng

last: LYU

first: Junbang

last: CHEN

first: Chunhua

last: HUANG

first: Hongyan

last: QIN

first: Chengyuan

last: LIN

first: Hor-Yue

last: TAN

first: Zhaoxiang

last: BIAN


title: Gene expression profiles of Control and FAK KO Th17 cells

city: Seoul

first: Gap Ryol

last: Lee

address: 35 Baekbeom-ro, Mapo-gu

department: Department of Life Science

country: South Korea

institute: Sogang University

summary: T helper type 17 (Th17) cells play critical roles in the pathogenesis of various autoimmune and inflammatory diseases; however, signaling pathways that affect Th17 cell differentiation are not fully understood. Here, we investigated whether focal adhesion kinase (FAK), an integrator of extracellular signals, regulates differentiation of Th17 cells. We measured alteration of gene expression in FAK-deficient Th17 cells compared to WT Th17 cells using RNA-sequencing.

overall_design: We isolated naïve CD4 T cells from Fakfl/fl mice and introduced a Cre recombinase-expressing vector into the cells to induce gene deletion (these cells are referred to Fak KO). These cells were stimulated with plate-bound anti-CD3ε (10 μg/ml) and soluble anti-CD28 (5 μg/ml) antibodies and cultured for 3 days under Th17-polarizing conditions. Then we harvested the cells and conducted RNA-sequencing (RNA-seq) to identify altered genes in Fak KO Th17 cells.

first: Hyeong Su

last: Kim

first: Ji Hyeon


title: The effects of YTHDC1 on liver function [YTHDC1 HKO]

city: Harbin

first: Zheng

last: Chen

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

country: China

institute: Harbin Institute of Technology

summary: The goal of this study is to investigate how YTHDC1 regulates liver function.

overall_design:
mRNA profiles in livers of Ythdc1flox/flox and Ythdc1-HKO mice were generated by deep sequencing using Illumina Novaseq 6000 platform (n=3 for each group).
Methods: Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany) from livers of Ythdc1flox/flox and Ythdc1-HKO mice at 9 weeks old. Three independent biological replicates for each group were used for RNA-seq. RNA-seq was performed by deep sequencing using an Illumina Novaseq 6000 platform. Paired-end clean reads were aligned to the mouse reference genome(GRCm38.p6) with Hisat2 v2.0.5, and the aligned reads were used to quantify mRNA expression by using featureCounts v1.5.0-p3.
Our study represents the first detailed analysis of liver transcriptomes from Ythdc1flox/flox and Ythdc1-HKO mice, generated by RNA-seq technology. The RNA-seq analysis showed that 1521 genes were downregulated and 1786 genes were upregulated in the livers of Ythdc1-HKO mice.

first: Xinzhi

last: Li


title: CircESR1 and HNRNPAB function in estrogen receptor positive (ER+) breast cancer [RNA-Seq]

status: Public on Jun 17 2025

city: Hefei

first: Xu

last: Junchao

state: Anhui

address: No. 443, Mount Huangshan Road, Daoxiangcun Street

institute: University of Science and Technology of China

summary: Breast cancer (BC) is the most prevailing type of cancer among women in the world. ERα protein, which is transcribed and translated by estrogen receptor gene ESR1, is one of the marker molecules for clinical classification of BC. However, whether circRNAs specifically expressed in hormone receptor-positive BC play a role which is independent of ERα (estrogen receptor alpha) protein activity and signaling pathways is unknown. Whether these circRNAs could impinge on the sensitivity of ER+ BC cells to the endocrine therapy and targeted drug therapy is also unexplored.By screening circRNAs involved in estrogen receptor (ER) signaling, circESR1 was identified as a circRNA exhibiting high specificity of expression in ER+ breast cancer. Our studies elucidate a novel signaling complex centering around circESR1 and HNRNPAB in ER+ breast cancer and suggest that circESR1 might represent a potential therapeutic target for this disease.

overall_design: Unbiased transcriptome sequencing (bulk RNA-seq) was performed to have identified differentially expressed genes (DEGs) due to circESR1 or HNRNPAB depletion in MCF-7 cells. In details, MCF-7 cells were infected circESR1 or HNRNPAB shRNAs with lentivirus. Then the RNA was isolated. Total RNA sample was extracted and quantified with OD 260/280 ratio > 1.8 and OD 230/260 ratio > 2 were sent to BGI Genomics (Shenzhen, China) for sequencing.

first: Junchao

first: Tao

last: Zhu


title: Paired single-cell and spatial transcriptional profiling reveals a central osteopontin macrophage response mediating tuberculous granuloma formation in humans and zebrafish [Spatial Transcriptomics]

status: Public on Jun 13 2025

city: Durham

first: Liuyang

last: Wang

state: NC

address: 213 Research Drive

institute: Duke University

summary: Mycobacterial granulomas are categorical manifestations of tuberculosis pathogenesis. They result from an ensemble of immune responses to Mycobacterium tuberculosis infection, but the identities, arrangement, cellular interactions and regulation of the cells that comprise them has thus far been incompletely understood. We conducted spatial and single-cell RNA sequencing of clinical granuloma biopsy specimens from tuberculosis patients. We found that granulomas consist of concentric transcriptional laminae surrounding areas of central necrosis. Gene expression programs associated with regional architecture were conserved among samples. We identified distinct populations of granuloma-associated stromal cells, fibroblasts, lymphocytes, mast cells, dendritic cells, neutrophils and macrophages. Populations further differentiate into multiple granuloma-specific states that correlate with location. We used inferential analysis to predict dominant granuloma cell-cell interactions, the activity of major signaling pathways, and differential transcription factor activities. Using spatial deconvolution, we mapped a conserved pattern of cellular organization dominated by macrophages rich in osteopontin/SPP1 expression. Trajectory analysis of macrophage subtypes mapped their differentiation and supported the importance of SPP1 to granuloma macrophage polarization.  Cumulatively, we have identified a dominant macrophage granuloma population as well as its central regulatory gene in human samples and confirmed its importance to granuloma biology in vivo.

overall_design: To examine the interdependence of lesional architecture and gene expression, we evaluated the whole spatial transcriptomes of 4 samples from four different patients at 55 µM resolution (~5-10 cells) using the 10x Genomics Visium v2 with CytAssist assay.

first: Charlie

middle: J

last: Pyle

first: David

last: Tobin


title: Natural and non-natural cytokine receptors generate diverse cell states to enhance T cell therapy [scRNA-seq]

status: Public on Jun 14 2025

city: Stanford

first: Yang

last: Zhao

state: CA

address: Beckman B169B, 279 Campus Drive

department: MCP

institute: Stanford University

summary: Cytokines augment T cell function, but the nature of the optimal signals are not well defined. We deployed orthogonal cytokine-receptors to diversify the JAK/STAT signaling profiles elicited by orthogonal IL-2. We designed chimeric receptors consisting of the orthogonal IL-2 receptor extracellular domain (ECD) fused to intracellular domains (ICDs) from receptors for other common gamma chain cytokines as well as ICDs from interferon receptor, IL-10 receptor and homodimeric receptor families not expressed on T cells. Such non-natural pairings with the common gamma chain expand the JAK/STAT signaling space in T cells. Natural and non-natural orthogonal chimeric receptors led to distinct T cell fates in tumors, including naturally occurring states (Tc2 differentiation driven by orthogonal chimeric IL4R) and synthetic states (myeloid-like T cells driven by orthogonal chimeric granulocyte colony stimulating factor receptor). The orthogonal chimeric IL22R (o22R) potently activated STAT-1, -3, -4, and -5, imparting T cells with stem-like and effector properties. The pronounced anti-tumor functionality mediated by o22R and oGCSFR was linked to remodeling of the exhaustion-associated epigenome. Our study broadens the cytokine receptor repertoire, providing novel solutions to overcome barriers for using engineered T cells to treat cancer.

overall_design: C57BL/6 mice were inoculated s.c. with B16F10 tumor cells (1 × 10^6), sublethally lymphodepleted by irradiation on day 7, and received i.v. adoptive transfer of 3 × 10^6 Pmel T cells (either untransduced or transduced with mo2R, mo4R, mo20R, mo22R, or moGCSFR) on day 8 post tumor followed by i.p. administration of MSA-oIL-2 (2.5 × 10^4 unit per day) or PBS control every other day until day 16. On day 17, mice were sacrificed, tumors were minced and dissociated using a mouse tumor dissociation kit (Miltenyi Biotec) and a gentleMACS Octo Dissociator (Miltenyi Biotec). Tumor-infiltrating lymphocytes (TILs) were first enriched by density gradient centrifugation against Percoll (Cytiva), and then stained with surface markers and DAPI (Thermo Fisher Scientific). Thy1.1+CD8+ or Thy1.1+CD8+ YFP+ T cells were sorted using an Aria II sorter (BD Biosciences) at the Stanford Share FACS Facility for Single cell RNA sequencing.

first: Aastha

last: Pal

first: Anusha

last: Kalbasi

first: Chris

last: Garcia


title: mRNA profiles of livers during postnatal development

summary: The goal of this study is to investigate how gene expression changes in the liver during postnatal development.

overall_design:
mRNA profiles in livers during postnatal development (day 1, day 10, day 20 and day 60 after birth) were generated by deep sequencing using Illumina Novaseq 6000 platform (n=3 for each group).
Methods: Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany) from livers of WT mice at day 1, day 10, day 20 and day 60 after birth. Three independent biological replicates for each group were used for RNA-seq. RNA-seq was performed by deep sequencing using an Illumina Novaseq 6000 platform. Paired-end clean reads were aligned to the mouse reference genome(GRCm38/mm10) with Hisat2 v2.0.5, and the aligned reads were used to quantify mRNA expression by using featureCounts v1.5.0-p3.
Our study represents the detailed analysis of liver transcriptomes from mouse livers during postnatal development, generated by RNA-seq technology.


title: Identification of mRNAs associated with YTHDC1 in primary hepatocytes

summary: The goal of this study is to identify mRNAs associated with YTHDC1 in primary hepatocytes.

overall_design:
Primary hepatocytes were infected with Ad-FLAG-YTHDC1 adenovirus overnight. RNA immunoprecipitation sequence (RIP-seq) assay was performed to identify mRNAs associated with YTHDC1 in primary hepatocytes.
Then, immunoprecipitated RNA or Input was used for library construction with NEB NextR Ultra™ RNA Library Prep Kit (New England Biolabs). Library quality was assessed on the Agilent Bioanalyzer 2100 system. The libraries were sequenced on an Illumina Novaseq 6000 platform with a paired-end read length of 150 bp according to the standard protocols. Raw data (raw reads) of fastq format were firstly processed using fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low- quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Index of the reference genome ( GRCm38/mm10) was built using BWA (v 0.7.12) and clean reads were aligned to the reference genome using BWA mem (v 0.7.12).
mRNAs associated with YTHDC1 in primary hepatocytes were characterized.

first: Xueying

first: Chunhong

last: Liu


title: Paired single-cell and spatial transcriptional profiling reveals a central osteopontin macrophage response mediating tuberculous granuloma formation in humans and zebrafish [scRNA-Seq]

overall_design: We processed tissue sections immediately adjacent to the Visium-imaged sections. We used these closely paired dissociated cells to determine at a single-cell level the transcriptional signature and cellular heterogeneity in human M. tb granulomas and then comprehensively mapped these transcriptional profiles onto the spatial analysis using deconvolution algorithms. To focus more deeply on granulomas in pulmonary tissue, the predominant site of TB disease, we processed 4 M. tb granuloma biopsy specimens resected from 3 patients with pulmonary TB.


title: Non-canonical AMPA receptor blockade reduces lymph node egress and neuroinflammation [Bulk RNA-seq]

city: Mainz

first: Neuroimmunology

last: Mainz

address: Langenbeckstr. 1

department: Neurology

country: Germany

institute: University Medical Center of the Johannes Gutenberg University Mainz

summary: Disturbances in the glutamatergic system have been linked to neuronal pathology. Investigating therapeutic translation, we discovered immune-related effects for the selective non-competitive AMPA receptor blocker perampanel in mouse models of multiple sclerosis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for EAE perampanel treated mice and controls

first: Beatrice

last: Wasser

first: Manuela

last: Ecker

first: Nicholas

last: Hanuscheck

first: Erik

last: Ellward

first: Muthuraman

last: Muthuraman

first: Mohammadsaleh

last: Oshaghi

first: Stefan

last: Bittner

first: Frauke

last: Zipp


title: Characterization of monocytes influence in human skin melanoma

status: Public on Jun 18 2025

city: Madrid

first: Rafael

last: Samaniego

address: Calle Dr Esquerdo 46

country: Spain

institute: Fundación para la Investigación Biomédica del Hospital Gregorio Marañón

summary: Tumor cells attract and dynamically interact with monocytes/macrophages, one of the more abundant cell types in the tumor microenvironment, to subvert their differentiation into tumor associated macrophages (TAMs), which mainly promote immunosuppression and neoplastic progression, but the mechanisms governing their protumoral activity are not completely understood. Thus, identifying molecular pathways promoted by monocytes that could be responsible for immune evasion and tumor malignicity may provide new therapeutic targets to improve the efficacy of immunotherapy of cancer.

overall_design: BLM and A375 human melanoma cell lines were coculture for 24h with CD14+ monocytes isolated from human PBMCs of three healthy donors. Also, CD14-CD3- tumor cells (TC) and CD3+ tumor infiltrated lymphocytes (TILs) were obtained skin melanoma primary tumors (CD14+ tumor-associated macrophages from the same tumors are available at GSE171277).

first: Alicia

last: Nieto-Valle

first: Celia

last: Barrio-Alonso

first: Alba

last: Gutiérrez-Seijo

first: Paloma

last: Sánchez-Mateos

first: Elena

last: García-Martínez


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

status: Public on Jun 04 2025

first: Wenqian

last: Li

address: Longzihu Road

institute: Anhui University of Chinese Medicine

summary: Natural product cinnamaldehyde has significant antifungal activities, and its inhibitory activity against Candida albicans has been reported. Up to now, there are few reports on the changes in the transcriptome of Candida albicans after cinnamaldehyde treatment. Here, RNA sequencing analysis of samples obtained from Candida albicans cells grown in the presence or absence of cinnamaldehyde was performed. A total of 123 differentially expressed genes were identified, of which 15 genes were up-regulated and 108 genes were down-regulated.

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 × 10^5 CFU/mL and incubated at 37 ℃ for 24 hours in the presence of cinnamaldehyde at 31.25 μg/mL. Considering that cinnamaldehyde was solubilized using DMSO, 5% DMSO treatment was used as a control group. 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 (control or cinnamaldehyde treated).

first: Zhaoling

last: Shi

first: Kelong

last: Ma


title: Methylation Profiling for Pediatric Pineal Parenchymal Tumors

status: Public on Jun 06 2025

city: Cairo

first: Shahenda

last: El-Naggar

address: 1 Sekket El Emam, El Madbah El Kadeem Yard, Sayeda Zeinab

department: Research Department

country: Egypt

institute: Children’s Cancer Hospital Egypt 57357

type: Methylation profiling by genome tiling array

summary: Pineal parenchymal body tumors are rare central nervous system tumors with a variety of presentations ranging from well-differentiated low-grade tumors to undifferentiated highly aggressive tumors. Recent molecular classification has described the heterogeneity among these tumors, particularly among pineoblastomas (PB) and papillary tumors of intermediate differentiation (PPTID). Herein, we describe the methylation profile for 20 pediatric pineal parenchymal tumors using Illumina Infinium Methylation EPIC BeadChip array and correlate it with the patients’ clinical data. Our findings support that these tumors are diverse, incorporating novel entities with distinct clinical features and the presence of medulloblastomas outside the posterior fossa.

overall_design: Our Study included 20 formalin-fixed-paraffin embedded (FFPE) tumor samples. DNA was isolated with QIAamp DNA FFPE tissue kit (Qiagen) and quantified using the DENOVIX Fluorometer (ds DNA High Sensitivity). DNA quality was determined using the Illumina FFPE QC kit (Illumina Inc.). Bisulfite conversion of the extracted DNA was performed using an EZ DNA methylation kit (D5002, Zymo Research). The bisulfite-converted DNA was restored using the Infinium HD FFPE DNA Restore Kit (WG-321-1002, Illumina Inc.). Restored bisulfite-converted DNA was hybridized to the Illumina Infinium Human Methylation EPIC 850K bead chips and scanned using the Illumina iScan microarray scanner according to the manufacturer's recommendations (Illumina Inc.).

first: Hend

last: Khaled

first: Amal

last: Mosaab

first: Hala

last: Taha

last: Refaat

first: Nada

last: Ashraf

first: Mohamed

middle: S

last: Zaghloul

last: El-Beltagy

first: Manal

last: Zamzam

first: Mark

middle: W

last: Kieran

first: Ahmed

last: El-Hemaly

first: Alaa

last: El-Haddad


title: Non-canonical AMPA receptor blockade reduces lymph node egress and neuroinflammation [scRNA-seq]

first: Neuroimmunology

last: Mainz

first: Beatrice

last: Wasser

first: Manuela

last: Ecker

first: Nicholas

last: Hanuscheck

first: Erik

last: Ellward

first: Muthuraman

last: Muthuraman

first: Mohammadsaleh

last: Oshaghi

first: Stefan

last: Bittner

first: Frauke

last: Zipp


title: CeRNA Microarray-Based Identification of Specific LncRNA Markers in Severe Tuberculosis for Early Diagnosis

status: Public on Jun 01 2025

city: Beijing

first: Siyu

last: Yao

address: Tongzhou District, No.9 Beiguan Street, Yard 1

institute: Beijing Chest Hospital Affiliated toCapital Medical University

summary: Tuberculosis (TB) is still one of the leading causes of death from a single infectious agent in the world.The progression of tuberculosis to severe disease is the main cause of death of tuberculosis patients. Early identification of severe tuberculosis is very important. LncRNA can be used as a potential marker in the diagnosis of tuberculosis, but there is a lack of research on lncRNA in the field of severe tuberculosis.This study aims to use CeRNA Microarray analysis to identify specific lncRNAs as potential biomarkers for severe tuberculosis diagnosis.

overall_design: Genome-wide lncRNA profiling of peripheral blood mononuclear cells (PBMCs) from severe tuberculosis (STB) patients, mild tuberculosis patients (MTB), and healthy controls (HCs) was conducted using the Agilent microarray technique. STB:8 samples;MTB:12 samples;HC:10 samples

first: Xiuxiu

last: Ji

first: Ruize

last: Wang

first: Liping

last: Pan

first: Qiuyue

last: Liu


title: Dietary fiber inulin enables intestinal microbiome to clear fructose and protect the host

status: Public on Jun 03 2025

city: Irvine

first: Cholsoon

last: Jang

address: 839 Health Sciences Rd

department: Biological Chemistry

institute: University of California Irvine

summary: Excessive consumption of fructose leads to various cardiometabolic diseases. However, inulin, dietary fiber composed of numerous fructose molecules, exerts health-beneficial effects. Here we report that inulin shifts fructose catabolism from the host organs to gut microbiome, reversing fructose-induced hyperlipidemia, hepatic steatosis and systemic glucose intolerance. Both simultaneous and delayed inulin intake enhances fructose clearance by the small intestinal microbiome, effectively reducing fructose dose reaching the liver and colon and thus suppressing hepatic lipogenesis. Inulin also activates the hepatic de novo serine synthesis pathway and cystine uptake to augment glutathione production and reduce oxidative stress. This dual effect of inulin is blocked by antibiotics and transmittable by fecal transplantation.  Moreover, inulin-enriched Bacteroides acidifaciens is protective against HFCS-induced lipogenesis. Our data provide mechanistic insights into how fructose-polymer fiber inulin rewires gut microbial fructose catabolism and protects the host from excessive fructose exposure, paving the way to mitigate fructose-induced metabolic disease.

overall_design: 8–week-old male C57BL/6 mice were fed either control (Research diets, D21050401) or 10% (gm%) inulin diet (Research diets, D21050402) for 30 weeks. To investigate the effect of inulin supplementation with HFCS, mice were assigned into five groups (n = 9): (1) consumed control diet with normal water (C); (2) inulin diet with normal water (I); (3) control diet with HFCS water (CF); (4) inulin diet with HFCS water (IF); (5) switched from control diet to inulin diet with continual provision of HFCS water (CIF). For HFCS water, mice were provided either normal water or 15% (weight/volume) 1:1 mixture of glucose and fructose in water to mimic high fructose corn syrup. After 30 weeks of feeding, liver tissues were quickly dissected and snap-frozen in liquid nitrogen with a pre-cooled Wollenberger clamp and subjected to RNA-sequencing.

first: Sunhee

last: Jung

first: Hosung

last: Bae

first: Won-Suk

last: Song

first: Yujin

last: Chun


title: Gene expression profile at single cell level from the brain at 3h, 2d, and 7d after hypoxic ischemic encephalopathy

city: Hangzhou

first: Jingyu

state: Zhejiang

address: No.688 Yuhangtang road

institute: Zhejiang University

summary: Hypoxic ischemic encephalopathy (HIE) causes brain paralysis. Here, we used single-cell RNA sequencing (snRNA-seq) to examine brain cell heterogeneity during the hyperacute (3 h), acute (2 d), and subacute (7 d) phases.

overall_design: All cells from the brains of sham rats and HIE rats were isolated and analyzed using scRNA-seq

first: Xianbo

last: Chen


title: Single-Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [scRNA-Seq]

status: Public on Jun 02 2025

city: Austin

first: Anna

last: Battenhouse

state: TX

address: 100 East 24th St., Stop A5000

department: Center for Biomedical Research Support

institute: The University of Texas at Austin

summary: Retinal ganglion cells (RGCs) are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not regenerate after injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC survival after injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals, zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection (ONT) using isl2b:eGFP transgenic fish line, single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3, a cell population having progenitor and regenerative identity.

overall_design: Seven single-cell RNA libraries were prepared from FACS-purified retinal ganglion cells (RGC) from pooled tissue from seven sets of adult zebrafish: four libraries from injured tissue after optic nerve transection at 2 timepoints: 1 and 7 days post-injury (dpi), and three libraries from uninjured tissue on the same days.

first: Ashrifa

last: Ali

first: Hannah

last: Schriever

first: Dennis

last: Kostka

first: Taka

last: Kuwajima

first: Kristen

last: Koenig

first: Jeffrey

last: Gross


title: NAT10 in Diabetic Cardiomyopathy in Exercise

city: Boston

first: Haobo

last: Li

state: MA

address: MEDR410 / Lunder Bldg Dock, 255 Charles St

department: Department of Anesthesia, Critical Care, and Pain Medicine

institute: Massachusetts General Hospital and Harvard Medical School

summary: To investigate the role of NAT10 in diabetic cardiomyopathy in response to exercise, 6-week-old NAT10 floxed mice were fed a high-fat diet (HFD) for 18 weeks followed by low doses of STZ injections, some of the mice were then injected with AAV9-cTnT-Cre to knockout NAT10 in cardiomyocytes. There mice were then subjected to either sedentary or eight weeks of treadmill exercise. We then performed gene expression profiling analysis using data obtained from RNA-seq from RNAs pulldown with an ac4C antibody.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from RNAs pulldown with an ac4C antibody from heart tissues from mice treated with control or NAT10 knockout with exercise.


title: Single-Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [RNA-Seq]

overall_design: Nine bulk RNA-seq libraries were prepared from FACS-purified retinal ganglion cells (RGC) from pooled tissue from nine sets of adult zebrafish: three libraries from injured tissue after optic nerve transection at each of 3 timepoints: 1, 5, and 7 days post-injury (dpi), and three from uninjured tissue on the same days.


title: Non-canonical AMPA receptor blockade reduces lymph node egress and neuroinflammation

status: Public on Jun 12 2025

first: Neuroimmunology

last: Mainz

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

overall_design: Refer to individual Series


title: ParBF DNA binding profiles from variants of the CTP binding motif

city: Toulouse

first: Jean-Yves

last: Bouet

address: 169 avenue Marianne Grunberg-Manago

country: France

institute: CNRS

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We report the genome-wide analysis from chromatin immunoprecipitated DNA (ChIP-sequencing) of the DNA binding pattern of ParBF (SopB) of plasmid F. This study, performed in E. coli, investigates the impact of mutations in the CTP binding motif BoxIII on ParBF DNA binding profiles in vivo. We found that ParBF-N153A allele binds to parS as WT but is impaired in clamp formation thus abolishing the long distance DNA binding on parS-proximal DNA. By contrast, ParBF-R156A DNA binding profile reveals that it binds to parS, converts to clamps that diffuse over several Kb and unbinds non-specific DNA in a similar way as WT. However, the reduction in ParB binding at proximity of parS revealed that ParBF-R156A is impaired in ParB-ParB interaction, thus preventing the assembly of ParB condensates.

overall_design: Chromatin immunoprecipitation DNA-sequencing for ParB of plasmid F (ParBF) in Escherichia coli. Biological replicates are labelled IP1 and IP2. Anti ParBF antibody is affinity purified before used.

first: Perrine

last: Revoil

first: Jerome

last: Rech

first: Delphine

last: Labourdette

first: Hicham

last: Sekkouri Alaoui


title: High Mobility Group Box protein 3 (HMGB3) facilitates DNA interstrand crosslink processing and double-strand break repair in human cells

summary: DNA damaging agents can contribute to genetic instability, and such agents are often used in cancer chemotherapeutic regimens due to their cytotoxicity. Thus, understanding the mechanisms involved in DNA damage processing can not only enhance our knowledge of basic DNA repair mechanisms, but may also be used to develop improved chemotherapeutic strategies to treat cancer. The high mobility group box protein 1 (HMGB1) is a known nucleotide excision repair (NER) co-factor, and its family member HMGB3 has been implicated in chemo-resistance in ovarian cancer. Here, we aim to understand the potential role(s) of HMGB3 in processing DNA damage. A potential role in NER was investigated using HMGB3 knockout human cell lines in response to UV damage. Interestingly, unlike HMGB1, HMGB3 does not appear to play a role in NER. Subsequently, potential roles in DNA interstrand crosslink (ICL) and DNA double-strand break (DSB) repair were investigated using mutagenesis assays, metaphase spreads, foci formation, a variety of DNA repair assays, and Tag-Seq analyses in human cells. We found evidence to suggest that HMGB3 is involved in the processing of both DSBs and ICLs in human cells. These novel results elucidate a role for HMGB3 in DNA damage repair, and surprisingly, also indicate a distinct role of HMGB3 in DNA damage repair from that of HMGB1. These findings advance our understanding of the role of HMGB3 in chemotherapeutic drug resistance and as a target for new chemotherapeutic strategies in the treatment of cancer.

overall_design: For TagSeq sequencing (a form of 3' RNA sequencing), four replicate libraries were prepared for Wild Type UNOS cells, and for each of three HMGB3 CRISPR Knock-out clones. Resulting sequences were analyzed for differentially expressed genes between the KOs and the WT.

first: Jillian

last: Dangerfield

first: Anirban

last: Mukherjee

first: Wade

last: Reh

first: Karen

last: Vasquez


title: Retinoic acid-regulated epigenetic marks identify Alx1 as a direct target gene required for optic cup formation [RNA-seq]

status: Public on May 31 2025

city: La Jolla

first: Gregg

last: Duester

address: 10901 North Torrey Pines Road

department: Center for Cardiovascular and Muscular Diseases

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: Retinoic acid (RA) is a transcriptional control agent that regulates several aspects of eye development including invagination of the optic vesicle to form the optic cup, although a target gene for this role has not been previously identified. As loss of RA synthesis in Rdh10 knockout embryos affects the expression levels of thousands of genes, a different approach is needed to identity genes that are directly regulated by RA. Here, we combined ChIP-seq for epigenetic marks with RNA-seq on eye tissue from wild-type embryos and Rdh10-/- embryos that exhibit failure in optic cup formation. We identified a small number of genes with decreased expression when RA is absent that also have decreased presence of a nearby epigenetic gene activation mark (H3K27ac). One such gene was Alx1 that also has an RA response element (RARE) located near the RA-regulated H3K27ac mark, providing strong evidence that RA directly activates Alx1. In situ hybridization studies showed that Rdh10-/- embryos exhibit a large decrease in eye Alx1 expression. CRISPR/Cas9 knockout of Alx1 resulted in a failure in optic cup formation, thus demonstrating that RA directly activates Alx1 in order to stimulate this stage of eye development.

overall_design: Gene expression comparison of Rdh10 KO and WT eye in mice using RNA-seq.

first: Marie

last: Berenguer


title: Assay for transposase-accessible chromatin-sequencing (ATAC-seq) of liver samples from  Ythdc1flox/flox and Ythdc1-HKO mice, respectively.

first: Zheng

last: Chen

summary: The goal of this study is to determine whether hepatic deletion of Ythdc1 affects chromatin accessibility.

overall_design:
To assess chromatin accessibility in the liver casued by hepatic deletion of Ythdc1, ATAC-seq analysis of liver samples in Ythdc1flox/flox and hepatocyte-specific Ythdc1 knockout (Ythdc1-HKO) mice was performed.
Each liver sample was pooled from four Ythdc1-HKO and Ythdc1flox/flox mice, respectively. Nuclei was extracted from liver samples, and the nuclei pellet was resuspended in the Tn5 transposase reaction mix. The transposition reaction was incubated at 37°C for 30 min. Equimolar Adapter1 and Adatper 2 were added after transposition, PCR was then performed to amplify the library. After the PCR reaction, libraries were purified with the AMPure beads and library quality was assessed with Qubit. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufactuer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina NovaSeq 6000 platform and 150 bp paired-end reads were generated. ATAC-seq analysis was performed using a standard protocol.
The chromatin accessibility in the livers of Ythdc1flox/flox and Ythdc1-HKO mice were characterized.

first: Xinzhi

first: Xueying

first: Chunhong

last: Liu


title: SUL1 deficiency reduces PKA activity to increase replicative lifespan in yeast Saccharomyces cerevisiae

city: Cheng

first: Ma

last: Meng

address: University of Electronic Science and Technology Shahe Campus

institute: University of Electronic Science and Technology of China

summary: The process of sulfate uptake plays a crucial role in cellular metabolism and growth. SUL1, a plasma membrane transporter responsible for regulating the entry of extracellular sulfate in S. cerevisiae. Our previous work verified SUL1 as a fundamental gene involved in the regulation of lifespan. This study aimed to undertake a more comprehensive analysis of the role of SUL1 in regulating longevity. Our data showed that that sulfate transport is not required for the effect of SUL1 deletion on increased longevity. The SUL1 mutant demonstrates decreased functionality within the PKA signaling pathway, resulting in a variety of effects, such as increased stress-protective trehalose and glycogen, enhanced autophagy, elevated expression of stress response genes, and reduced expression of ribosomal genes. Concurrently, the observed increase in lifespan resulting from the deletion of SUL1 may be partially attributed to the stimulation of autophagy and MSN2-mediated transcriptional activity. The findings of this study provide additional evidence for the association between sulfate transporter and longevity, thereby identifying a novel potential intervention target for extending lifespan.

overall_design: To investigate the mechanism by which SUL1 mutations extend lifespan, exponential phase cells from the SUL1 mutant、SUL2 mutant、 E427 mutant and wild-type (WT) groups were harvested and subjected to total RNA extraction for the construction of mRNA libraries intended for sequencing analysis. The WT strain was utilized as a control group, with three biological replicates per group.

first: Juan

last: Long

first: Hao

first: Jing

last: Yang


title: High-density cultures (3D-cultures) associated therapy resistance in AML THP-1 cells

status: Public on Jun 09 2025

city: Puschino

first: Kirill

last: Krasnov

state: Moscow region

address: institutskay 3

country: Russia

institute: ITEB RAS

summary: Acute myeloid leukemia (AML) is an aggressive hematologic malignancy characterized by the rapid proliferation of immature myeloid cells in the bone marrow, leading to impaired hematopoiesis and life-threatening complications. Despite advances in chemotherapy, targeted therapy, and stem cell transplantation, treatment resistance remains a major clinical challenge, contributing to high relapse rates and poor survival outcomes. Understanding the mechanisms of resistance — including genetic mutations, epigenetic alterations, and microenvironmental interactions — is crucial for developing more effective therapies. Investigating how AML cells develop treatment resistance, particularly under pro-inflammatory conditions, may reveal novel therapeutic targets and improve patient prognosis. Our study focuses on resistance mechanisms in AML cells under density-induced sterile pro-inflammatory conditions (modelled via high-density culture, HDC). This approach aims to identify key molecular pathways associated with therapy resistance in AML.

overall_design: Comparison of RNA-seq profiles between: (1) AML THP-1 cells under high-density culture (HDC; reversible therapy resistance via sterile pro-inflammatory signaling), (2) AML THP-1 cells under low-density culture (LDC; non-inflammatory condition), and (3) mutant macrophage-like AML THP-1 (THP-1ad) cells derived from HDC (exhibiting fully resistant, differentiated phenotype)

first: Fadeev

last: Roman

first: Kobyakova

middle: I

last: Margarita

first: Lomovskaya

middle: V

last: Yana

first: Krasnov

last: Kirill

first: Meshcheriakova

last: Elena


title: TDP-43 loss induces cryptic polyadenylation in ALS/FTD [sknbe2-curve-kd-1-vs-ctl]

status: Public on May 30 2025

city: Leuven

first: Sam

last: Bryce-Smith

address: Herestraat 49

department: VIB-KU Leuven Center for Brain and Disease Research

country: Belgium

institute: KU Leuven

summary: Nuclear depletion and cytoplasmic aggregation of the RNA-binding protein TDP-43 is the hallmark of ALS, occurring in over 97% of cases. A key consequence of TDP-43 nuclear loss is the de-repression of cryptic exons. Whilst TDP-43 regulated cryptic splicing is increasingly well catalogued, cryptic alternative polyadenylation (APA) events, which define the 3’ end of last exons, have been largely overlooked, especially when not associated with novel upstream splice junctions. We developed a bioinformatic pipeline to reliably identify distinct APA event types: alternative last exons (ALE), 3’UTR extensions (3’Ext) and ‘ composite ’ intronic polyadenylation (IPA) events. We identified novel neuronal cryptic APA sites induced by TDP-43 loss of function by systematically applying our pipeline to a compendium of publicly available and in house datasets. We find that TDP-43 binding sites and target motifs are enriched at these cryptic events and that TDP-43 can have both repressive and enhancing action on APA. Importantly, all categories of cryptic APA can also be identified in ALS and FTD post mortem brain regions with TDP-43 proteinopathy underlining their potential disease relevance. RNA-seq and Ribo-seq analyses indicate that distinct cryptic APA categories have different downstream effects on transcript and translation. Intriguingly, cryptic 3’Exts occur in multiple transcription factors, such as ELK1 , SIX3, and TLX1, and lead to an increase in RNA stability. 3’Exts are localised to the cytoplasm and neurites and translated leading to an increase in wild-type protein levels. In summary, we demonstrate that TDP-43 nuclear depletion induces a novel category of cryptic RNA processing events and we expand the palette of TDP-43 loss consequences by showing this can also lead to an increase in normal protein translation.

overall_design: short-read bulk RNA-sequencing of IPSC-derived cortical neurons and neuroblastoma cell lines (SH-SY5Y and SK-N-BE(2)) with and without TDP-43 knockdown

first: Matteo

last: Zanovello

first: Matthew

last: Keuss

first: Anna-Leigh

last: Brown

first: Alla

last: Mikheenko


title: TDP-43 loss induces cryptic polyadenylation in ALS/FTD [humphrey-i3-cortical]

overall_design: short-read bulk RNA-sequencing of day 30 IPSC-derived cortical neurons with and without TDP-43 knockdown (6 controls, 6 TDP-43 knockdowns)

first: Jack

last: Humphrey


title: TDP-43 loss induces cryptic polyadenylation in ALS/FTD [slamseq-i3-cortical]

overall_design: SLAM-seq of IPSC-derived cortical neurons with and without TDP-43 knockdown. Day 7 neurons were cultured with a uridine analogue 4sU to label newly synthesised RNA over a time course (sampled at 0, 1, 4, 8, 12 and 24hrs). Isolated RNA is treated with iodoacetamide to alkylate the incorporated 4sU (to mimic a cytosine) and then standard bulk short-read RNA-seq library preparation is performed.

first: Sarah

last: Hill


title: TDP-43 loss induces cryptic polyadenylation in ALS/FTD [shsy5y-curve-kd-075-vs-ctl]

overall_design: short-read bulk RNA-sequencing of the SH-SY5Y neuroblastoma cell line with and without TDP-43 knockdown (3 controls, 3 KD samples)


title: TDP-43 loss induces cryptic polyadenylation in ALS/FTD [zanovello-i3-cortical-tdpkd-vs-tdpctl]

overall_design: short-read bulk RNA-sequencing of IPSC-derived cortical neurons with and without TDP-43 knockdown


title: TDP-43 loss induces cryptic polyadenylation in ALS/FTD [shsy5y-chx-tdpkd-vs-ctl]

overall_design: short-read bulk RNA-sequencing of the SH-SY5Y neuroblastoma cell line with and without TDP-43 knockdown (4 controls, 4 knockdowns)


title: Three germline lncRNAs promote PUM protein condensation and germline differentiation

status: Public on May 29 2025

city: Jerusalem

first: Yonatan

last: Tzur

address: Givat-Ram

country: Israel

institute: Hebrew University of Jerusalem

summary: Long-non-coding RNAs (lncRNAs) are highly expressed in gonads yet, given the lack of fertility defects in most knockouts, their role is unclear. Here, we report the overlapping roles of three lncRNAs in Caenorhabditis elegans fertility, whereby they bind and sequester FBF-2, an inhibitor of germ-cell differentiation. Deletion of the lncRNAs leads to additive reduction in progenitor-cells and progeny. FBF-2 destabilizes mRNAs, and in the lncRNAs deletion strain, the level of these mRNAs is significantly lower. FBF-2 is present in germ-cells, both diffused in the cytoplasm and in peri-nuclear condensates, and lncRNAs deletion reduces FBF-2 condensation. Moreover, the deletion reduces FBF-2 association to P granules, evolutionarily conserved phase-separated condensates. Our work demonstrates that lncRNAs cooperate to establish optimal fertility; hence the full effect is only evident in multiple knockouts. These findings support a model that the lncRNAs spatially restricts pro-proliferation factors into phase-separated granules and release mRNAs required for differentiation.

overall_design:
Comparative transcriptomics between WT and fbf-2 mutants and between WT and a mutant in 3 lincRNA genes

Compartive transcriptomics between fbf-1 and fbf-1Xtriple mutants

first: Roni

last: Falk

first: Noa

last: Gilad

first: Hanna

last: Achache

first: Ilanit

last: Sopher-Levi

first: Yisrael

last: Rappaport

first: Reut

last: Shantai

first: Hasan

last: Ishtayeh

first: Kayla

last: Nennig-Kniaz

first: Laura

last: Wolovelsky

first: Oren

last: Ram


title: Characterization of the meningeal leukocytes in 3xTg-AD mice

city: Verona

first: Gabriela

last: Constantin

state: Verona

address: Strada le Grazie 8

department: Department of Medicine, Division of General Pathology

country: Italy

institute: University of Verona

summary: We characterize the meningeal leukocyte (CD45+ cells) in wild-type and 3xTg-AD mice, a transgenic model of Alzheimer's disease (AD).

overall_design: Pools of 8 female mice (3xTg-AD or wild-type) were used for single-cell RNA-Seq (scRNAseq) analysis. Leukocytes isolated from the meninges were washed with PBS, and labeled with an anti CD45–BV480 antibody (Becton Dickinson). The cells were re-suspended in PBS supplemented with 10% FBS), and viable CD45HIGH cells were sorted on a FACSAria Fusion (Becton Dickinson). Both the 3xTg-AD and wild-type samples consisted of > 98% viable cells.

first: Constantin

last: Gabriela

first: Zenaro

last: Elena


title: RNAseq profiling of back dermis from epidermal-specific SPRY1-deficient (Spry1 cKO) mice and control mice

status: Public on May 27 2025

city: hangzhou

first: Fan

last: Xu

state: zhejiang

address: 88 Jiefang Road,Shangcheng District Hangzhou,China

institute: Zhejiang university

summary: Spry1 cKO mice were found spontaneously developed psoriasis-like skin inflammation and arthritis.To further investigate the gene expression differences between the back dermis of Spry1 cKO mice and control mice, RNAseq was performed.

overall_design: The back skin of Spry1 cKO mice and control mice were harvested after tamoxifen administration, and the dermis was separated after digestion with 5% dispase overnight at 4°C. Then RNA-seq was performed on total RNA from the back dermis.

first: Ying-Zhe

last: Cui

first: Xiao-Yong

last: Man


title: TransTag enables simple and efficient transgene mapping in zebrafish via tagmentation

city: Denton

first: Fanju

last: Meng

state: Texas

address: 1155 Union Circle #305220

department: Department of Biological Sciences

institute: University of North Texas

summary: Zebrafish has become a preeminent model for developmental biology research, largely due to the ease of transgenesis. Despite widespread usage of transgenic lines, mapping of transgene insertion sites is rare, which raises complications involving potential local chromatin influences on transgene expression, off-target effects, and issues with allelic variation. To address these short-comings, we introduce TransTag, a simple and efficient method utilizing Tn5 transposase-mediated tagmentation, for streamlined identification of Tol2-based transgene insertion sites in zebrafish. TransTag is straightforward to perform and can identify insertion sites without the need for alignment of raw sequencing data. We also provide a detailed protocol for TransTag, a step-by-step guide for data analysis, and a user-friendly Shiny app, making transgene mapping achievable at low cost for researchers without programming expertise. Altogether, TransTag emerges as a valuable tool to enhance the precision and utility of transgenesis studies by providing essential chromosome-specific information on transgene locations.

overall_design: TransTag libraries for several transgenic zebrafish strains were generated and analyzed to identify transgene insertion sites.

first: Paige

last: Schneider

first: Xiaolu

last: Wei

first: Krishan

last: Ariyasiri

first: Marnie

middle: E

last: Halpern

first: Patrick

last: Murphy


title: Characterization of the brain infiltrating leukocytes in 3xTg-AD mice [Pools of 8 female mice brain]

summary: We characterize the brain infiltrating leukocyte (CD45high cells) in wild-type and 3xTg-AD mice, a transgenic model of Alzheimer's disease (AD).

overall_design: Pools of 8 female mice (3xTg-AD or wild-type) were used for single-cell RNA-Seq (scRNAseq) analysis. Leukocytes isolated from the brain were washed with PBS, and labeled with an anti CD45–BV480 antibody (Becton Dickinson). The cells were re-suspended in PBS supplemented with 10% FBS), and viable CD45HIGH cells were sorted on a FACSAria Fusion (Becton Dickinson). Both the 3xTg-AD and wild-type samples consisted of > 98% viable cells.


title: CHIP-seq analysis of H3K27ac in papillary thyroid carcinoma patient's tissues and paired normal tissues

city: Tianjin

first: Xiukun

last: Hou

address: Huanhu Road

institute: Tianjin Cancer Institute and Hospital

summary: To identify the super enhancers, we performed Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3K27ac in in papillary thyroid carcinoma patient's tissues

overall_design: H3K27ac ChIP-seq on normal and tumor tissue

first: Wei

last: Zhang


title: RNA-seq of papillary thyroid carcinoma (PTC)  patient's tissues and paired normal tissues

summary: To describe the transcriptome of PTC, we performed RNAseq analysis of PTC  patient's tissues and paired normal tissues

overall_design: RNA-seq

first: Xianhui

last: Ruan


title: H3K27ac ChIP-seq and RNA-seq of papillary thyroid carcinoma patient's tissues and paired normal tissues

status: Public on May 26 2025

overall_design: Refer to individual Series


title: KDM5 demethylases suppress R-loop-mediated “viral mimicry” and DNA damage in breast cancer cells [CUT&Tag_H3K4me3]

status: Public on May 19 2025

city: San Diego

first: Marie

last: Classon

address: 10555 Science Center Dr

institute: Pfizer

summary: Tumors with low expression of Interferon-Stimulated Genes (ISG) and Antigen Presentation (AP) genes respond relatively poorly to current immunotherapies. One of the early hallmarks of cancer is DNA hypomethylation in genomic repeat regions, resulting in the expression of normally silenced endogenous “viral” elements.  Such epigenetic changes have the potential to augment anti-tumor immune responses as well as reduce tumor cell fitness through the generation of aberrant nucleic acid species (NAS) and consequent activation of NAS-sensing pathways.  Therefore, tumor evolution should favor additional selective events that suppress NAS generation, possibly yielding specific therapeutic vulnerabilities.  Here, we show that the Lysine Demethylase 5 (KDM5) family of epigenetic regulatory enzymes suppress R-loop formation in genomic repeat regions in cancer cells.  We find that KDM5 inhibition in luminal breast cancer cells results in R-loop-mediated DNA damage, reduced cell fitness and an increase in ISG and AP signatures as well as cell surface Major Histocompatibility Complex (MHC) class I, mediated by RNA:DNA hybrid activation of the CGAS/STING pathway. KDM5 inhibition does not result in DNA damage or activation of the CGAS/STING pathway in normal breast epithelial cells, suggesting that KDM5 inhibitors may enable a wide therapeutic window in this setting, as compared to STING agonists or Type I Interferons. These findings provide new insights into the interplay between epigenetic regulation of genomic repeats, R-loop formation, innate immunity, and cell fitness in the context of cancer evolution and therapeutic vulnerability.

overall_design: Cut-and-Tag profiling of the histone modification H3K4me3 in HCC1428 cells treated with KDM5 inhibitor C48 for 5 days

first: Lena

last: Lau

first: Kurt

last: Henderson

first: Ahu

last: Turkoz

first: Sara

last: Linker

first: Dorte

last: Schlesinger

first: Brad

last: Townsley

first: Brian

last: Egan

first: Shoba

last: Regunathan

first: Robert

last: Rollins

first: Xianju

last: Bi

first: Zhijian

last: Chen

first: Oleg

last: Brodsky

first: Clifford

last: Restaino

first: Murali

last: Gururajan

first: Kristen

last: Jensen-Pergakes

first: Anders

last: Malarstig

first: Chames

last: Kermi

first: Paul

last: Moore


title: KDM5 demethylases suppress R-loop-mediated “viral mimicry” and DNA damage in breast cancer cells [RNA-Seq]

first: Marie

last: Classon

overall_design: RNA-seq profiling of HCC1428 cells treated with KDM5 inhibitor C48 for 2 and 7 days

first: Lena

last: Lau

first: Kurt

last: Henderson


title: SOX9 is a driver of a stem-like transcriptional state and platinum resistance in high-grade serous ovarian cancer [Unenriched_Tumor]

status: Public on May 16 2025

city: Chicago

first: Mazhar

last: Adli

state: IL

address: 303 E. Superior St

department: Department of Obstetrics & Gynecology

institute: Northwestern University

summary: Resistance to platinum-based chemotherapies remains a formidable challenge to the treatment of high-grade serous ovarian cancer (HGSOC). The complex and multifaceted nature of this cell state has been thought to originate in a small subpopulation of inherently resistant cancer stem cells (CSCs) in naïve tumors. However, there is increasing evidence that the chemoresistance state can be transiently acquired by non-stem cancer cells as well. Regardless of the route to chemoresistance, the key regulators of this process are poorly understood. Here, we use patient-derived single-cell RNA-Seq, multimodal sequencing, tumor microarray staining, and endogenous epigenetic modulation to show that SOX9 is a key driver of chemoresistance in HGSOC. We show that genetic or epigenetic upregulation of SOX9 is sufficient to induce chemoresistance in multiple ovarian cancer cell lines. Moreover, this upregulation induces the formation of a stem-like subpopulation and can significantly decrease tumor chemosensitivity in vivo. Mechanistically, SOX9 expression drives global transcriptional divergence and reprograms the transcriptional program of naïve cells into a stem-like state. Supporting this, our multi-omic single-cell analysis identified a rare cluster of SOX9-expressing cells that are highly enriched for CSCs and chemoresistance-associated stress gene modules in a naïve tumor. Notably, single cell profiles of naïve cells show that chemo treatment results in rapid population-level expression of SOX9 that enriches for a stem-like transcriptional state. Altogether, these findings implicate SOX9 as a critical regulator of early steps of transcriptional reprogramming that leads to chemoresistance through a cancer stem-like state in HGSOC.

overall_design: Multimodal single-cell RNA and ATAC seq of a whole tissue human high grade serous ovarian tumor before patient received neo-adjuvant chemotherapy

first: Alexander

last: Duval


title: Folliculin deletion in the mouse kidney results in cystogenesis of the loops of Henle via aberrant TFEB activation

status: Public on May 23 2025

city: Kuamomoto

first: Shunsuke

last: Tanigawa

state: Kumamoto

address: 2-2-1 Chuou-ku honjyo

department: Institute of Molecular Embryology and Genetics

country: Japan

institute: Kumamoto University

summary: The mammalian kidney contains numerous nephrons connected to the collecting ducts, and each nephron consists of a glomerulus, a proximal tubule, the loop of Henle (LoH), and a distal tubule. Folliculin (Flcn) is a causative gene for Birt-Hogg-Dube (BHD) syndrome, which is characterized by a variety of symptoms including renal cysts and cancers. Although deletion of Flcn in the mouse collecting duct has been reported to result in cyst formation, its precise role in the nephron remains unclear. We report here that nephron-specific Flcn knockout mice exhibit cystogenesis along the entire nephron segments, most prominent in the LoH, preceded by an irregularly shaped lumen lined by enlarged epithelia. Single-cell RNA sequencing revealed many upregulated genes, especially in the mutant LoH. These genes include those related to lysosomal activity and mTORC1 activation and are likely targets of TFE3/TFEB. While the double Flcn/Tfe3 knockout only ameliorates the glomerular cysts, the double Flcn/Tfeb knockout dramatically reverses most of the phenotypes along the entire nephron. Thus, Flcn deletion leads to cystogenesis via aberrant TFEB activation. Our findings reveal the essential role of the Flcn-TFEB-mTORC1 signaling pathway in nephron development, particularly in LoH, and shed light on the initial disease state of BHD syndrome.

overall_design: To investigate the gene expression profiles upon Flcn deletion in all nephron lineages, scRNA-seq analysis were performed using Flcn heterozygous (Six2Cre; Flcn flox/+) and Flcn homozygous (Six2Cre; Flcn flox/flox) neonatal kidneys (P0).

first: Ola

last: Shalaby

first: Koichiro

last: Miike

first: Masaya

last: Baba

first: Ryuichi

last: Nishinakamura


title: KDM5 demethylases suppress R-loop-mediated “viral mimicry” and DNA damage in breast cancer cells [CUT&Tag_S96]

overall_design: Cut-and-Tag profiling of R-loops using S9.6 antibody in HCC1428 cells treated with KDM5 inhibitor C48 for 5 days

first: Ahu

last: Turkoz

first: Sara

last: Linker

first: Dorte

last: Schlesinger

first: Brad

last: Townsley

first: Brian

last: Egan

first: Shoba

last: Regunathan

first: Robert

last: Rollins

first: Xianju

last: Bi

first: Zhijian

last: Chen

first: Oleg

last: Brodsky


title: LLC cancer cells from primary tumors from Padi4f/f-Mrp8Cre- (WT) and Padi4f/f-Mrp8Cre+ (PAD4-DN) mice bulk RNA-seq data

status: Public on May 15 2025

city: Baltimore

first: Jose

last: Adrover

state: Maryland

address: 855 N Wolfe St

department: Cell Biology

institute: Johns Hopkins University

overall_design: Tomato-expressing LLC cells sorted from primary tumors from WT (Mrp8Cre-, Padi4fl/fl) and PAD4-DN (Mrp8Cre+, Padi4fl/fl) mice and subjected to bulk RNAseq.

first: Mikala

last: Egeblad


title: Single-cell RNA sequencing profiling of periarticular tissue from epidermal-specific SPRY1-deficient (Spry1 cKO) mice and control mice

first: Fan

last: Xu

summary: Spry1 cKO mice were found spontaneously developed psoriasis-like skin inflammation and arthritis.To further investigate the periarticular immune microenvironment in paws, single-cell RNA sequencing of the periarticular tissue from Spry1 cKO and control mice was performed.

overall_design: The periarticular tissue of Spry1 cKO mice and control mice were harvested after tamoxifen administration, and single-cell suspensions of periarticular tissue were prepared using collagenase IV. To obtain sufficient immune cells for analysis, four mice were pooled as one sample for the control group (12 control mice in total for n=3), and then CD45+ and CD45- cells were sorted and mixed at a ratio of 3:1 in both groups for scRNA-seq analysis.

first: Ying-Zhe

last: Cui

first: Xiao-Yong

last: Man


title: Prenatal VEGF Nano-Delivery Reverses Congenital Diaphragmatic Hernia-Associated Pulmonary Abnormalities

status: Public on May 17 2025

city: London

first: Federica

last: Michielin

address: 30 Guilford Street

department: GOS ICH

country: United Kingdom

institute: University College London

summary: Congenital diaphragmatic hernia (CDH) affects 1-2 in 5,000 neonates who are born with hypoplastic lungs leading to significant morbidity and mortality. In severe cases tracheal occlusion (TO) can be offered to promote lung growth through airway stretch, but such growth remains limited. Vascular endothelial growth factor (VEGF), a key mediator of normal lung development, is downregulated in animal models of CDH, but its role in CDH-associated lung pathology in humans is not known. Using 18-22 post-conception week fetal lungs from CDH patients, we demonstrated for the first time that lung hypoplasia in this setting is associated with impaired VEGF expression and reduced pulmonary epithelial cell proliferation. We then developed a human ex vivo model of fetal lung compression relevant to CDH, in which a mechanical constraint was added to cultured lung fragments. Our model recapitulated impaired branching morphogenesis observed in CDH fetal lungs, and scRNAseq revealed significant reduction of the proliferative potential of terminal bud epithelial progenitors with concomitant reduction in expression of VEGF. Importantly, the exogenous supplementation of recombinant VEGF in this setting induced a significant increase of terminal bud progenitor cell proliferation, comparable to non-compressed control tissue. Finally, we developed a novel therapeutic agent delivery platform by conjugating recombinant VEGF on the surface of nanoparticles (nanodiamonds; ND-VEGF). In utero, intratracheal administration of ND-VEGF into the in vivo TO Nitrofen rat model of CDH resulted in lung growth as well as pulmonary arterial remodelling leading to histological appearances comparable to healthy controls. The beneficial effects of ND-VEGF were abrogated by co-administration of a selective VEGF-receptor-2 (KDR/Flk1) inhibitor and were not observed when unconjugated VEGF was delivered. This innovative approach could have a significant impact on the treatment of CDH.

overall_design: We combined culture of whole embryonic mouse lungs with a recently developed technology that can generate stiff barriers through selective crosslinking of Cumarin HCC-conjugated 8-arm-polyethylene glycol gel (PEG-HCC) under a two-photon microscope. Mouse lungs were freshly isolated from fetuses at 12.5 days of gestation (E12.5) and embedded in Matrigel drops placed on top of a porous cell culture insert in Air-liquid Interphase (ALI). The next day (Day 0), a 20% PEG-HCC solution was dispersed into the Matrigel drop and selectively crosslinked to surround the lungs and inhibit their growth over a total of 2 days. Control lungs had the same amount of PEG-HCC solution added to the Matrigel, but this was not crosslinked with the two-photon laser. 4 replicates were analyzed by bulk RNA-seq at Day 0, Day 2 under control conditions, Day 2 under compression conditions.

first: Stavros

middle: P

last: Loukogeorgakis

first: Noura

last: Al-Juffali

first: Julio

last: Jimenez

first: Soichi

last: Shibuya

first: Jessica

last: Allen-Hyttinen

first: Patrice

last: Eastwood

first: Ahmed

last: Alhendi

first: Joseph

last: Davidson

first: Eleonora

last: Naldi

first: Panagiotis

last: Maghsoudlou

first: Alfonso

last: Tedeschi

first: Sahira

last: Khalaf

first: Aziza

last: Khabbush

first: Manuela

last: Plate

first: Camila

last: Fachin

first: Andre

last: Dos Santos Dias

first: Nikhil

last: Sindhwani

first: Dominic

last: Scaglioni

first: Theodoros

last: Xenakis

first: Neil

last: Sebire

first: Monica

last: Giomo

first: Simon

last: Eaton

first: Jaan

last: Toelen

first: Camilla

last: Luni

first: Piero

last: Pavan

first: Peter

last: Carmeliet

first: Francesca

last: Russo

first: Samuel

last: Janes

first: Marko

middle: Z

last: Nikolic

first: Nicola

last: Elvassore

first: Jan

last: Deprest

first: Paolo

last: De Coppi


title: CITE-Seq of tumors from 4T1-tumor bearing mice

first: Jose

last: Adrover

summary: CITE-Seq of sorted cells from the tumor of 4T1-bearing mice to study immune cell composition.

overall_design: CITE-Seq was performed on sorted cells from the tumors of 4T1-bearing mice. CITE-Seq was performed using TotalSeq-B Mouse Universal Cocktail, V1.0.

first: Mikala

last: Egeblad


title: Orthotopic 4T1 tumors spatial transcriptomics

summary: 4T1 tumors, 4 weeks after implantation were excised and analyzed using the 10X Visium technology.

overall_design: FFPE tissue blocks were cut down to approximately 6.5 mm x 6.5 mm in size and sectioned onto the capture areas of the Visium slide according to 10X Genomics Tissue Preparation Guide CG000408. Slides were then deparaffinized and H&E-stained according to the 10X Genomics Demonstrated Protocol CG000409 and imaged at the Animal & Tissue Imaging Core Facility at CSHL. After imaging, the tissue was decrosslinked and probe hybridization with the Visium Mouse Transcriptome Probe Kit (PN-1000365, 10X Genomics) was performed overnight at 50°C. Probe ligation, probe release and extension, and library preparation were performed according to manufacturer’s instructions, and final libraries were sequenced on a NextSeq 500 to target 20,000 reads per spot. Sequencing data were processed with Space Ranger version 2.0.0 (10X Genomics).


title: SOX9 is a driver of a stem-like transcriptional state and platinum resistance in high-grade serous ovarian cancer

first: Mazhar

last: Adli

overall_design: Multimodal single-cell RNA and ATAC seq of a epithelial-cell-enriched human high grade serous ovarian tumor before patient received neo-adjuvant chemotherapy

first: Alexander

last: Duval


title: Effect of constant inflammation on in vitro expanded adipose-derived mesenchymal stromal cells

city: Copenhagen

first: Tu

last: Hu

address: 5 Artillerivej

department: Infectious Disease Immunology

country: Denmark

institute: Statens Serum Institut

summary: Human adipose-derived mesenchymal stromal cells (AD-MSCs) are known for their immunomodulatory responses to inflammation, a key trait for their therapeutic use in tissue injury and chronic inflammatory diseases. However, the effects of constant inflammation on their transcriptomic profile, proliferative capacity, and immunosuppressive potential remain largely unexplored. To investigate this, we evaluated the in vitro response of human AD-MSCs from three donors expanded across seven passages under, non-inflamed (DMEM), acute (IFNγ-24h) and constant (IFNγ-C) inflammatory conditions. Bulk RNA-sequencing results demonstrated that AD-MSCs respond significantly to inflammatory stimuli. Both acute and constant inflammation induced extensive transcriptomic alterations, with differentially expressed genes related to cell cycle regulation, DNA replication, metabolism, and immunomodulation. Notably, constant inflammation was associated with a transcriptomic shift toward oxidative phosphorylation (OXPHOS). Moreover, microscopy analysis revealed a significant reduction in AD-MSCs proliferative capacity under constant inflammation, as evidenced by lower cumulative population doubling and the appearance of senescence‐like morphological changes in early passages when compared to non-inflamed (DMEM) and acute inflammatory (IFNγ‐24h) conditions. Despite proliferation was impaired, co‐culture assays with PBMCs demonstrated that under constant inflammation AD-MSCs immunosuppressive potential was maintained in early and late passages. Therefore, our results provide novel insights into the dual effects of constant inflammation on AD-MSCs, impairing cell proliferation while maintaining their immunosuppressive capacity. Understanding AD-MSCs’ behaviour in chronically inflamed microenvironments is essential for optimizing AD-MSCs' clinical applications.

overall_design: Adipose-derived mesenchymal stromal cells (AD-MSCs) were isolated from human subcutaneous adipose tissue of three independent donors and expanded from passage 0 to passage 7 under three conditions: non-inflamed medium (DMEM), 24-hour interferon-gamma (IFNγ) exposure, or continuous IFNγ treatment. At each passage, cells were grown to approximately 80% confluency, harvested by trypsinization, and pelleted for RNA extraction using the RNeasy Mini Kit (Qiagen). RNA purity and concentration were assessed by NanoDrop, and RNA integrity was confirmed by TapeStation (RIN ≥7). High-quality RNA was used for cDNA library preparations, which were sequenced at BGI using a paired-end protocol (100-bp reads). Raw FASTQ files were produced for downstream differential expression and pathway analyses, and pertinent metadata, including donor identity, passage number, and treatment condition, were recorded for each sample.

first: Marina

middle: R

last: Galera

first: Lisa

last: Harth

first: Mariana

last: Bronze

first: Lea

last: Munthe-Fog

first: Jesper

last: Svalgaard

first: Anders

last: Woetmann


title: Age-associated dysregulation of post-synaptic mitochondria perturbs re-innervation kinetics

city: Ann Arbor

first: Carlos

middle: Andres

last: Aguilar

state: MI

address: 2200 Bonisteel Blvd

department: Biomedical Engineering

institute: University of Michigan

summary: Age-associated degeneration of neuromuscular junctions (NMJs) contributes to sarcopenia and motor decline, yet the mechanisms linking mitochondrial dysfunction to impaired NMJ regeneration in aging remain poorly defined. Here, we demonstrate that post-synaptic mitochondria are significantly diminished in both quantity and bioenergetic function in aged skeletal muscle, correlating with increased denervation and delayed reinnervation following nerve injury. Single-nucleus RNA sequencing of myofibers before and after sciatic nerve crush revealed that sub-synaptic myonuclei in aged muscle exhibit attenuated induction of mitochondrial gene programs, including oxidative phosphorylation, biogenesis, and import. To test whether these deficits are causal, we developed a muscle-specific CRISPR genome editing approach targeting CHCHD2 and CHCHD10—two nuclear-encoded mitochondrial proteins that localize to the intermembrane space and interact with the mitochondrial contact site and cristae organizing system (MICOS). Knockout of CHCHD2/CHCHD10 in young muscle recapitulated aged phenotypes, including mitochondrial disorganization, reduced ATP production, NMJ fragmentation, and delayed reinnervation. Transcriptional profiling of NMJ nuclei from knockout muscles revealed impaired pseudotime progression, failure to activate mitochondrial remodeling programs, and elevated stress signatures. These findings establish a critical role for sub-synaptic mitochondrial integrity in sustaining NMJ stability and regenerative capacity and identify CHCH domain-containing proteins as key regulators of post-synaptic mitochondrial function during aging and injury.

overall_design: Tibialis anterior muscles from young (2–5 months) and aged (23–29 months) mice were collected at 0, 7, and 14 days after sciatic nerve crush injury. Samples include uninjured and post-injury timepoints. Experimental groups consist of age-matched controls and injured muscles, with additional groups receiving intramuscular injections of AAV targeting CHCHD2/CHCHD10 or saline (PBS). All conditions include biological replicates. Young and aged timepoints include 2–3 biological replicates per group, and AAV vs. PBS conditions include 3–4 replicates per timepoint. Both multiplexed and non-multiplexed libraries were generated across batches.

first: Steve

middle: D

last: Guzman

first: Paula

last: Fraczek

first: Klimentini

last: itsani

first: Esraa

last: Furati

first: Grace

last: Kenney

first: Joe

last: Chakkalakal


title: Microvascular endothelial cells license APS vasculopathy through YAP1- and CCN2-mediated signaling

status: Public on May 14 2025

first: hui

last: shi

address: 5560 Medical Science Research Building-II 1150 W Medical Center Drive

institute: Division of Rheumatology, Department of Internal Medicine, University of Michigan

summary: Antiphospholipid syndrome (APS)-associated vasculopathy is heralded by abnormal proliferation of endothelial and smooth muscle cells, leading to small blood vessel occlusion in the skin, kidneys, and heart, amongst other organs. The underlying mechanisms remain unclear, and targeted treatment options for patients with APS are lacking. To identify and analyze APS microvascular endothelial cells (MVECs), skin biopsies of patients with APS complicated by livedo racemosa were characterized using single-cell RNA sequencing (scRNA-seq). Increased expression of CCN1 and CCN2 were discovered and further confirmed in APS skin by microscopy, and in APS plasma by ELISA. Exposure of healthy MVECs to patient IgG triggered CCN1 and CCN2 upregulation via yes-associated protein (YAP1)-mediated signaling. CCN2 originating from APS IgG-stimulated MVECs led to the proliferation and migration of vascular smooth muscle cells, which were blocked by the anti-CCN2 antibody, pamrevlumab. We further observed increased expression of CCN1 and CCN2, along with evidence of YAP1 nuclear translocation, in kidney vessels of APS nephropathy biopsies. Finally, CCN2 inhibition with pamrevlumab significantly reduced neointima thickening and cell proliferation in a mouse model of APS IgG-accelerated neointima formation. Together, this study revealed activation of YAP1-mediated signaling in APS dermal microvessels and demonstrated that the YAP1 target CCN2 plays a role in facilitating pro-proliferative communication between MVECs and VSMCs. These findings offer insights into the cellular and molecular mechanisms underlying APS vasculopathy and provide potential therapeutic targets for patients.

overall_design: Epidermal and dermal cells were isolated from skin biopsies from the upper thighs of three APS patients and four healthy volunteers, mixed 1:1 and analyzed using scRNA-seq.

first: Hui

last: Shi

first: Jason S

last: Knight


title: Spatial transcriptomics advances the use of canine patients in cancer research: a study of tumor-bearing pet dogs enrolled in an osteosarcoma clinical trial

status: Public on May 13 2025

city: Bethesda

first: Anjali

last: Garg

address: Building 10, Room 1B53

department: Comparative Oncology Program,NCI

institute: National Institute of Health

summary: Pet dogs spontaneously develop many of the same tumor types as humans including osteosarcoma. Utilizing the canine patient model facilitates the study of novel therapeutics and biomarkers within the context of spontaneous carcinogenesis, inclusive of treatment resistance, metastatic progression and immune responses that mirror that observed in human cancers. Recent advances in spatial transcriptomics have improved our ability to utilize formalin-fixed paraffin-embedded tissues collected at canine autopsy. These techniques allow the canine model to be investigated alongside murine models to inform human cancer research. Herein we present the first application of the GeoMx Canine Cancer Atlas to outcome-linked samples from canine patients enrolled in an osteosarcoma clinical trial.

overall_design: A tissue microarray (TMA) of primary osteosarcoma samples was assayed using the GeoMx Digital Spatial Profiler. Samples were stratified by disease-free interval (DFI). Patients within the upper and lower tertiles were assigned to the High (n = 8) and Low DFI (n = 8) groups, respectively. Analyses included the identification of differentially expressed genes, pathway enrichment, and cell deconvolution.

first: Jessica

last: Beck

first: Church

last: Sarah

first: Christina

last: Mazcko

first: Amy

last: LeBlanc


title: Ly6C-low and Ly6C-high neutrophils bulk RNA-seq data

first: Jose

middle: M

last: Adrover

summary: Neutrophils (single cells - Ly6G+ cells) from 4T1 tumor bearing mice were sorted based on Ly6C high or low expression and sequenced.

overall_design: Ly6C-high and Ly6C-low neutrophils fom 4T1 tumor-bearing mice were sorted. Then total RNA was extracted using a Qiagen RNeasy Plus kit, according to the manufacturer’s instructions. We then measured the concentration of the total RNA using Qubit (Thermo Fisher) and Agilent RNA 6000 Nano kit (Cat. ID: 5067-1511) to analyze its quality. Libraries were made using the Kapa mRNA Hyper prep protocol: the mRNA is captured with oligo-dT beads and then fragmented using heat and magnesium. The first cDNA strand is synthesized using random priming. Then, this step is followed by a combined second strand synthesis and A-tailing, which converts the cDNA:RNA hybrid to double-stranded cDNA (dscDNA), incorporates dUTP into the second cDNA strand, and adds dAMP to the 3’ ends of the resulting dscDNA. The next steps are Illumina adaptor ligation and then library amplification using high-fidelity, low-bias PCR. The strand marked with dUTP is not amplified, allowing strand-specific sequencing. As starting material, we used 100 ng of total RNA in 50 μl of DNase-free water. For fragmentation, we incubated the samples 6 minutes at 85°C (fragments of 300–400 bp). For PCR enrichment, we used 13 cycles. Quality control for the final libraries was done using Qubit (DNA HS assay) and Bioanalyzer (DNA HS assay), then we pooled the samples and checked the final library using the Kapa qPCR. Sequencing was done using the Illumina NextSeq 500/550 Mid Output Kit v2.5 (~24M single-end 75-cycles reads for each sample).

first: Mikala

last: Egeblad


title: Protein-primed DNA homopolymer synthesis by an antiviral reverse transcriptase [RIP-seq]

status: Public on May 09 2025

city: New York

first: Samuel

last: Sternberg

address: 701 W. 168th Street, HHSC 726

institute: Columbia University

summary: Bacteria defend themselves from viral predation using diverse immune systems, many of which sense and target foreign DNA for degradation. Defense-associated reverse transcriptase (DRT) systems provide an intriguing counterpoint to this strategy by leveraging DNA synthesis instead. We and others recently showed that DRT2 systems use an RNA template to assemble a de novo gene, leading to expression of an antiviral effector protein, Neo. It remains unknown whether similar mechanisms of defense are employed by other related DRT families. Focusing on DRT9, here we uncover an unprecedented mechanism of DNA homopolymer synthesis, in which viral infection triggers polydeoxyadenylate (poly-dA) accumulation in the cell to drive abortive infection and population-level immunity. Cryo-EM structures reveal how a conserved noncoding RNA serves as both a structural scaffold and reverse transcription template to direct hexameric complex assembly and RNA-templated poly-dA synthesis. Remarkably, biochemical and functional experiments identify conserved tyrosine residues within the reverse transcriptase itself that prime DNA synthesis, leading to the formation of high-molecular weight protein-DNA covalent adducts. Synthesis of poly-dA in vivo is regulated by the competing activities of phage-encoded triggers and host-encoded silencers of DRT9. Collectively, our work unveils a novel nucleic acid-driven defense system that expands the paradigm of bacterial immunity and broadens the known functions of reverse transcriptases.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: We performed RNA immunoprecipitation and sequencing (RIP-seq) on DRT9 reverse transcriptases in E. coli cells to profile their RNA binding activities in vivo. We also performed RIP-seq using mutant DRT9 systems.

first: Stephen

last: Tang

first: Rimantė

last: Žedaveinytė

first: Nathaniel

last: Burman

first: Shishir

last: Pandey

first: Josephine

middle: L

last: Ramirez

first: Louie

last: Kulber

first: Tanner

last: Wiegand

first: Royce

last: Wilkinson

first: Yanzhe

last: Ma

first: Dennis

last: Zhang

first: George

last: Lampe

first: Mirela

last: Berisa

first: Marko

last: Jovanovic

first: Blake

last: Wiedenheft

middle: H


title: Protein-primed DNA homopolymer synthesis by an antiviral reverse transcriptase [cDIP-seq]

platform_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: We applied a recently developed technique, termed cDNA immunoprecipitation and sequencing (cDIP-seq), to DRT9 reverse transcriptases in E. coli cells to identify their cDNA products in vivo. We also performed cDIP-seq using mutant DRT9 systems.


title: RAF conformational autoinhibition and 14-3-3 proteins promote paradoxical activation

status: Public on May 08 2025

city: La Jolla

first: Jingting

last: Yu

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

summary: RAF kinase inhibitors can, in some conditions, increase RAF kinase signaling. This process, which is commonly referred to as “paradoxical activation” (PA), is incompletely understood. RAF kinases are regulated by autoinhibitory conformational changes, and the role of these conformational changes in PA is unclear. Our mathematical investigations reveal that a dynamic equilibrium between autoinhibited and non-autoinhibited forms of RAF, along with the RAF inhibitor stabilization of the non-autoinhibited form, can be sufficient to create PA. Using both computational and experimental methods we demonstrate that 14-3-3 proteins, which stabilize both RAF autoinhibition and RAF dimerization, potentiate PA. Our model led us to hypothesize that increased 14-3-3 expression would amplify PA for the third generation RAF inhibitors that normally display minimal to no PA. Our subsequent experiments find that 14-3-3 overexpression increases PA, increases RAF dimerization, and promotes resistance to these inhibitors, effectively “breaking” these “paradox breaker” and pan-RAF inhibitors. Overall, this work reveals a robust mechanism for PA based solely on equilibrium dynamics of canonical interactions in RAF signaling.

overall_design: mRNA profiles of SK-MEL-2 human melanoma cells in media supplemented with vemurafenib, media supplemented with PLX8394, and regular growth media at day 3, 7, 14 and 21.

first: Gaurav

last: Mendiratta

first: Kodye

last: Abbott

first: Yao-Cheng

last: Li

first: Jianfeng

last: Huang

first: Maxim

middle: N

last: Shokhirev

first: Thomas

last: McFall

first: Geoffrey

last: Wahl

first: Edward

middle: C

last: Stites


title: Autophagy related 14 regulates liver homeostasis and function

status: Public on May 07 2025

city: Indianapolis

first: Xiaocheng

middle: Charlie

last: Dong

state: IN

address: 635 Barnhill Dr, MS 1021D

department: Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

summary: Autophagy regulated 14 (ATG14) is a key regulator of autophagy; however, its role in the liver remains poorly understood. This study aimed to investigate the hepatocyte-specific function of ATG14 in vivo. We generated Atg14 hepatocyte-specific knockout (HepKO) mice using adeno-associated virus (AAV) to deliver thyroxine-binding globulin (TBG) gene promoter-driven Cre into Atg14 floxed mice at an adult age and fed control and knockout mice with a Western diet for 4 weeks.

overall_design: RNA-seq analysis of liver tissue samples from control and Atg14 HepKO mice

first: X


title: Control of citrate utilization by Candida albicans Adr1

status: Public on May 05 2025

city: Athens

first: Amelia

last: White

state: GA

address: 120 E Green Street

department: Microbiology

institute: University of Georgia

summary: Opportunistic fungal pathogen Candida albicans often encounters host niches where it must survive on alternative carbon sources alone. In Saccharomyces cerevisiae, transcription factor Adr1 activates genes required for acetate and glycerol utilization. However, previous researchers found that CaADR1 deletion mutants have robust growth on acetate and glycerol. We have found that Adr1 is required for growth on citrate. This phenotype is manifested among multiple strains isolated from all known host niches. RNA sequencing analyses of adr1Δ/Δ and wild-type strains show that Adr1 is required for expression of genes within the TCA cycle and gluconeogenesis. Major targets include enzymes Mdh1 and Pck1. Unexpectedly, one of the most downregulated genes is not within the central metabolic pathway. HGT17 is a putative glucose transporter. Phenotypic analyses support the hypothesis that Hgt17 is able to transport citrate.

overall_design: RNA-seq profiling of WT C. albicans cells and their knockdown derivatives (adr1ΔΔ and hgt17ΔΔ). Cells were grown for 4h at 37 degrees in either YNB+1% citrate or YNB + 1% acetate

first: Amelia M

first: Aaron P

last: Mitchell


title: Protein-primed DNA homopolymer synthesis by an antiviral reverse transcriptase [RNA-seq]

first: Samuel

last: Sternberg

overall_design: We performed total RNA-seq in E. coli cells expressing SenDRT9 infected with either WT or escape mutant T5 phage to assess phage transcript levels.

first: Stephen

last: Tang

first: Rimantė

last: Žedaveinytė

first: Nathaniel

last: Burman

first: Shishir

last: Pandey

first: Josephine

last: Ramirez

first: Louie

last: Kulber

first: Tanner

last: Wiegand

first: Royce

middle: A

last: Wilkinson

first: Yanzhe

last: Ma

first: Dennis

middle: J

last: Zhang

first: George

first: Mirela


title: The ImmgenT Open-Source project

city: Boston

first: Liang

last: Yang

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

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

overall_design: The immgen T OpenSource Project is a collaborative effort involving 100 participants across 41 laboratories, working together to create the most comprehensive atlas of T cells in the mouse immune system. Leveraging a common data generation pipeline, the goal is to profile T cells in every body location, capturing their diverse states in response to a broad range of immunological challenges and physiological states (infection, autoimmune, tumor, aging), and how specific gene programs drive this diversity. Profiling was performed at the single-cell level, with multimodal mRNA, surface protein (CITE-seq/TotalSeq, 128 antibody panel), and TCR-VDJ (paired TCRα/TCRβ). Please refer to individual series for a description of each experiment.


title: Bisphenol A-induced renal metabolic disruption: Insights into MAPK-mediated steroid hormone dysregulation from transcriptomic and metabolomic analyses

city: Taiyuan

first: Rui

last: Gao

address: Shanxi University of Medical Sciences, 98 University Street, Yuci District, Jinzhong City, Shanxi Province

institute: shanxi medical university

summary: After long-term exposure of BPA, human is probably suffering from invisible renal injury and metabolic disruption, while its linked intricate gene transcriptional mechanisms warrant more conclusive evidence.  Comprehensive analysis utilizing transcriptomics and metabolomics were used to elucidate the transcriptional mechanisms regulating metabolic homeostasis involved in BPA-induced nephrotoxicity. Here, six-week-old male ICR (CD1) mice were randomly divided into vehicle group with 10 mice and BPA exposure group with 10 mice (five mice per cage). The mice in the exposure group received a daily gavage of BPA dissolved in an aqueous solution containing 0.1% ethanol at the dose of 50 μg/kg/d, which is the tolerable daily intake (TDI) dose of BPA. The mice in the vehicle group received the same dose of aqueous solution containing 0.1% ethanol. After 6-week exposure, the mice were euthanized and left kidney were tissues were frozen with liquid nitrogen and used for RNA transcriptome sequencing.

overall_design: RNA-seq profiling of kidney after BPA exposure


title: Genome-wide screen uncovers novel host factors for L-A virus maintenance and a mutualistic-symbiosis relationship in yeast

status: Public on May 01 2025

city: Taipei

first: Tien-Hsien

last: Chang

address: 128 Academia Road, Section 2, Nankang

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

summary: Background:  Viruses are traditionally viewed as intracellular parasites that exploit host resources to propagate, often at the host’s expense.  However, emerging evidence suggests more nuanced interactions, including potential mutualism.  The L-A double-stranded RNA (dsRNA) virus, a non-lytic, cytoplasmic virus commonly found in Saccharomyces cerevisiae, presents an intriguing case, as it lacks clear pathogenic effects in the absence of its M1 satellite. Results:  To address how and why L-A persistently resides in its yeast host, we conducted a genome-wide screen using yeast deletion and temperature-sensitive mutant collections, covering approximately 93% of annotated genes, to identify host factors essential for L-A maintenance.  This screen revealed 96 genes spanning diverse biological processes. Transcriptomic profiling indicated that L-A presence alters the host stress-response gene expression.  Furthermore, competitive fitness assays under stress conditions demonstrated that L-A can enhance host resilience, suggesting a mutualistic relationship. Conclusion:  Our findings uncover a previously unrecognized virus-host mutualism, wherein L-A benefits its host under environmental stress.  These results not only expand our understanding of persistent viral infections in eukaryotes but also challenge the canonical view of viruses as purely parasitic, offering new insights into virus-host co-evolution and endogenous viral persistence.

overall_design: RNA-Seq profiling of nine wildtype (WT) yeast Saccharomyces cerevisiae BY4741 strains that endogenous harboring different expression of L-A virus (without L-A , mid level of L-A, highly expression level of L-A virus strains).  Librart construction using rRNA depleted and poly(A) RNA enriched method respectively.

first: Wan-Yi

last: Hsiao