title: Six3 and Six6 jointly regulate the identities and developmental trajectories of multipotent retinal progenitor cells in the embryonic mouse retina

city: The Bronx

first: Alexander

last: Ferrena

address: 1301 Morris Park Ave

department: Genetics

institute: Albert Einstein College of Medicine

summary: Regulation of retinal differentiation in mammals is not adequately understood. Using single-cell RNA sequencing of control and Six3 and Six6 compound-mutant mouse embryonic eye-cups, we identified cell clusters and developmental trajectories jointly regulated by transcription factor Six3 and its close paralog Six6. In control retinas, naïve retinal progenitor cells had two major trajectories leading to ciliary margin cells and retinal neurons, respectively. The ciliary margin trajectory was directly from naïve retinal progenitor cells at G1 phase whereas the neuronal trajectory was through a neurogenic state marked by Atoh7 expression. Upon Six3 and Six6 dual deficiencies, both naïve and neurogenic retinal progenitors were defective, ciliary margin differentiation was enhanced, and multi-lineage neuronal differentiation was disrupted. An ectopic neuronal trajectory lacking the Atoh7+ state led to ectopic neurons. Additionally, opposing gradients of Wnt and Fgf signaling were perturbed. Our findings provide deeper insight into molecular mechanisms underlying early retinal differentiation in mammals.

overall_design: Mouse embryos from the mating between Six3F/F;Six6-/-;a-Cre male and Six3F/F;Six6+/- female were harvested at E13.5. Intact eye cups containing the neural retina and lens were dissected out from neighboring tissues. Eye cups from an embryo with the genotype of Six3F/F;Six6-/-;a-Cre were identified based on GFP+ rosettes in the retinas under a stereo fluorescence microscope. The correlation between GFP+ rosettes and the genotype of Six3F/F;Six6-/-;a-Cre was previously established in pilot studies. Eye cups from an embryo without GFP were used as a control. Tails of the selected embryos were collected for genotyping. Then, eye cups were dissociated into single cells using activated Papain (Worthington Biochemical) for cell capture using the 10x Chromium fluid device, targeting 10,000 cells for each sample. Genotyping of the embryos confirmed the genotype of Six3F/F;Six6-/-;a-Cre for DKO retinas and the genotype of Six3+/-;Six6+/- for the littermate control. Previous phenotype analysis indicates that embryos with the genotype of Six3+/-;Six6+/- are nearly indistinguishable from wildtype embryos (Diacou et al., 2018). Captured cells were used for library preparation using the 10x Genomics Single Cell 3’ kit (version 3).

first: Xusheng

last: Zhang

first: Rupendra

last: Shrestha

first: Deyou

last: Zheng

first: Wei


title: SETDB1 suppresses interferon responses and NK cell-mediated immunosurveillance specifically in monocytic AML: Gene expression profiles of cSAM leukemia cells with Setdb1 depletion [RNA-seq]

status: Public on Aug 03 2024

city: Tokyo

first: Yu-Hsuan

last: Chang

address: 4-6-1 Shirokanedai, Minato-ku

country: Japan

institute: The University of Tokyo

type: Expression profiling by high throughput sequencing

summary: Monocytic acute myeloid leukemia (AML) responds poorly to current treatments, including venetoclax-based therapy. We conducted in vivo and in vitro CRISPR/Cas9 library screenings using a mouse monocytic AML model, and identified SETDB1 and its binding partners (ATF7IP and TRIM33) as crucial tumor promoters in vivo. The growth-inhibitory effect of Setdb1 depletion in vivo was mainly dependent on NK cell-mediated cytotoxicity. Mechanistically, SETDB1 depletion upregulated interferon-stimulated genes and NKG2D ligands through demethylation of histone H3 Lys9 at the monocyte-specific enhancer regions, thereby enhancing their immunogenicity to NK cells and intrinsic apoptosis. Importantly, these effects were not observed in non-monocytic leukemia cells. We also identified the expression of MNDA and its murine counterpart Ifi203 as biomarkers to predict the sensitivity of each AML to SETDB1 depletion. Our study highlights the critical and selective role of SETDB1 in monocytic AML and underscores its potential as a therapeutic target for current unmet needs.

overall_design: To assess the molecular changes induced by Setdb1 depletion in mouse cSAM leukemia cells (transformed by SETBP1 and ASXL1 mutations), we examined gene expression profiles of cSAM cells with non-targeting control or Setdb1-targeting sgRNA by RNA-seq. cSAM cells were transduced with sgRNA (coexpress puromycin) plasmids and performed bulk RNA-seq after 1 µg/ml puromycin selection for 4 days.

first: Susumu

last: Goyama


title: Spatial Transcriptomics-based Identification of Molecular Markers for Nanomedicine Distribution in Tumor Tissue

status: Public on Aug 04 2024

city: Seoul

first: Jeongbin

last: Park

state: Not US or Canada

address: 23, Sinhyeon-ro 38beon-gil, Siheung-si, Gyeonggi-do, 14957, Rep. of KOREA

department: Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea

country: South Korea

institute: Seoul National University

summary: To elucidate the factors that determine nanomedicine tumor uptake, we developed a molecular marker identification platform by integrating microscopic fluorescence images of nanomedicine distribution with spatial transcriptomics (ST) information. When this approach is applied to PEGylated liposomes, molecular markers related to hypoxia, glucose metabolism and apoptosis can be identified as being related to the intratumoral distribution of the nanomedicine. We expect that our method can be applied to explain the distribution of a wide range of nanomedicines, and furthermore, the data obtained from this analysis can be used in precise utilization of the nanomedicine.

overall_design: Examination of a spatial transcriptomics library generated with the 10x Genomics visium platform and the corresponding  fluorescence drug map of a 4T1 solid tumor.

first: Jinyeong

last: Choi

first: Jae Eun

last: Lee

first: Hongyoon

first: Hyung-Jun

last: Im


title: Association of immune evasion in myeloid sarcomas with disease manifestation and patients’ survival

city: Halle (Saale)

first: Marcus

last: Bauer

address: Magdeburger Str.

department: Institute of Pathology

country: Germany

institute: Martin Luther University Halle-Wittenberg

summary: Myeloid sarcomas (MS) comprise rare extramedullary manifestations of myeloid neoplasms (MN) with poor patients’ outcome. While the clinical relevance of the tumor microenvironment (TME) is well established in many malignancies, there exists limited information in MS. Therefore, the expression of the human leukocyte antigen class I (HLA-I) antigens, HLA-I antigen processing and presenting machinery (APM) components and the composition of the tumor microenvironment (TME) were analyzed. RNAseq analysis of a subset of 10 MS patients with preserved and reduced HLA-I HC expression revealed 150 differentially expressed genes in significant reduced expression of inflammatory response genes was found in HLA-I HC high samples.

overall_design: Differential expression from HLA-I_high vs HLA-I_low myeloid sarcoma samples


title: Intergrated single-cell chromatin and transcriptomic analyses of the human skin experienced radiotherapy from cancer patients (multiome)

status: Public on Aug 02 2024

city: Stockholm

first: Ning

last: Xu Landén

address: K2 Medicin, Solna, K2 Derm o Ven Xu Landén N

country: Sweden

institute: Karolinska Institutet

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Long-term toxicities caused by cancer treatments have recently gained increasing recognition due to a steadily growing population of cancer survivors. Radiotherapy (RT) is a common treatment known to unintentionally harm surrounding normal tissues including the skin, hindering wound healing even years after treatment. Our study aimed to elucidate the underlying mechanisms of these late-onset adverse effects caused by RT. By comparing paired skin biopsies from previously irradiated (RT+) and non-irradiated (RT-) sites in breast cancer survivors who underwent RT years ago, we discovered compromised wound healing capacity and impaired fibroblast functions in the RT+ skin. By employing ATAC-seq, we identified altered chromatin landscapes in RT+ fibroblasts, pinpointing THBS1 as a crucial epigenetically primed wound repair-related gene. Further confirmation of THBS1's significance during wound repair came from single-cell RNA-sequencing and spatial transcriptomic analysis of human wounds. Remarkably, heightened and sustained THBS1 expression was observed in RT+ fibroblasts in both mouse and human radiation wound models, leading to impaired fibroblast motility and contractility. Encouragingly, our study found that treatment with anti-THBS1 antibodies promoted ex vivo wound closure in RT+ skin from breast cancer survivors. These findings indicate that dermal fibroblasts retain a long-term radiation memory recorded in the form of epigenetic changes. Targeting this maladaptive epigenetic memory shows promise for mitigating the late-onset adverse effects caused by RT, offering potential solutions to improve the quality of life for cancer survivors.

overall_design: We obtained human irradiated or non-irradiated skin from cancer patients who underwent radiotherapy.  To investigate the 'radiation memory' that might be harmful, we conducted single-cell RNA sequencing and ATAC sequencing on these samples.

first: Xiaowei

last: Bian

first: Yongjian

last: Chen

middle: X

last: Landén


title: Epigenetic memory of radiotherapy in dermal fibroblasts impairs wound repair capacity in cancer survivors (RNA-Seq)

overall_design: RNA-seq of human dermal fibroblast isolated from previously irradiated or non-irradiated areas of the same cancer patient. RNA-seq of human fibroblasts transfected with CRISPR-dCas9 targeting THBS1 or CRISPR-dCas9 empty vector. RNA-seq of human dermal fibroblast isolated from previously irradiated or non-irradiated areas of the same cancer patient, treated with or without TGFb.

first: Minna

last: Piipponen

first: Zhuang

last: Liu


title: FuHsi Maintains Nucleolar Structure and Initiates Nucleolar Biogenesis.

city: Nanjing

first: Shan

last: Gao

address: No. 2 Sipailou, Xuanwu District

country: China

institute: Southeast University

summary: We identify a previously uncharacterized human nucleoli-enriched protein FuHsi. FuHsi is an essential nucleolar molecule that regulates nucleolar biogenesis and mouse development.

overall_design: To identify the potential function of FuHsi in nucleolus, we performed expression profiling analysis on FuHsi-knockdown (KD) cells.

first: Xiaohui

last: Yang

first: Xiaodong

last: Wang

first: Ao

last: Ding

first: Songzhe

last: Wu

first: Xianting

last: Huang

first: Tianyou

last: Cheng

first: Liqiang

last: Duan

first: Shuwen

first: Jihang

first: Chi

first: Weihu

last: Ma

first: Qi

first: Ya

last: Wen

first: Xiaofeng

last: Zhu


title: Human cytomegalovirus hijacks L1 retrotransposon to fuel its heterogeneity

first: Dohoon

last: Lee

address: 1, Gwanak-ro, Gwanak-gu

department: Bioinformatics Institute

summary: Human Cytomegalovirus (HCMV) causes severe morbidity and mortality in an immune-compromised or immune-naïve host. Among DNA viruses, the genetic diversity of HCMV is unexpectedly high and comparable to those of RNA viruses, which hinders the development of effective vaccines and causes the emergence of antiviral resistance. However, little is known about how HCMV acquires genetic variation. Here, we propose an evolution strategy of HCMV, that exploits host “jumping DNA” L1 retrotransposon as a mutagen. We found that HCMV infection switches on L1 expression by upregulating transcription factors YY1 and RUNX3. Furthermore, HCMV DNA processivity factor, UL44 recruits L1 ribonucleoproteins to viral replication compartments and induces DNA damage to its genome. Deep-sequencing analysis of cultured HCMV genome revealed that L1 retrotransposon facilitates mutation burden on the viral genome. Indeed, laboratory adaptation of HCMV to fibroblasts is only observed upon active L1 expression. These findings demonstrate the evolution mechanism and molecular insights of how HCMV acquires genetic fitness by the hijacking of host L1 retrotransposon.

overall_design: Chromatin accessibility profiling of HCMV-infected and non-infected U373MG cells by ATAC-seq.

first: Sung-Yeon

last: Hwang

first: Sun

last: Kim

first: Kwangseog

last: Ahn


title: Transcriptome analysis of Aomsn2 in nematode-trapping fungus Arthrobotrys oligospora

city: Kunming City, Yunnan Province

first: Liu

last: Qianqian

address: No.2 Cuihu North Road, Wuhua District

institute: Yunnan University

summary: Transcriptomic analysis revealed that differentially expressed genes in the absence of Aomsn2 were involved in  TCA cycle, fatty acid degradation, oxidative phosphorylation.

overall_design: Examination of differential genes in the WT and ΔAomsn2 mutant strains and prediction of multiple cytological processes that may affect trap formation in Arthrobotrys oligospora.

first: Qianqian

first: KeXin

last: Jiang

first: Jinkui


title: Effect of compounds (9, 13, 20 and 21) on the HIV-1 transcription in TZM-bl cells infected with HIV-1NL4-3

status: Public on Aug 01 2024

city: Cheongju

first: YoungHyun

last: Shin

address: Osongsaengmyeong 2-ro

institute: Korea National Institute of Health

summary: We developed a cellular screening system capable of simultaneously evaluating the functional activities of Tat-induced LTR transcription and general cellular expression. Herein, we identified and optimized novel HIV-1 Tat inhibitory compounds that contain an oxadiazole core. To assess the inhibitory effect of our lead compounds on Tat-mediated HIV-1 transcription, we performed RNA-seq analyses of the HIV-1 transcripts in the compound-treated HIV-1-infected cells. The read counts of the transcripts mapped to the HIV-1 genome were substantially reduced in the compound 9- or 13-treated cells; however, the decrease of the read counts was not observed in the HIV-1 infected cells with the ineffective compounds (20 and 21). These data indicate that the viral transcription step is a target for our lead compounds.

overall_design: Novel oxadiazole compounds that inhibit HIV-1 Tat-mediated viral transcription were identified. To elucidate the Molecular mechanism underlying the Tat inhibition of compounds, we performed the level of viral transcripts using an RNA-seq analysis gene expression of our lead compounds treated-HIV-1 infected cells. Comparative gene expression profiling analysis of RNA-seq data for DMSO and compounds (9, 13, 20 and 21) treated cells.

first: Sang-Yeop

first: Cheol-Hee

last: Yoon


title: Combination anti-PD-1 and anti-CTLA-4 therapy generates waves of clonal responses that include progenitor-exhausted CD8 T cells [dataset 4]

city: Philadelphia

first: Alexander

middle: C

state: PA

address: 421 Curie Boulevard

department: Department of Hematology/Oncology

country: USA

institute: University of Pennsylvania

summary: Combination checkpoint blockade with anti-PD-1 and anti-CTLA-4 antibodies has shown promising efficacy in melanoma. However, the underlying mechanism in humans remains unclear. We performed RNA+TCR single-cell analysis across time in 36 stage IV melanoma patients treated with anti-PD-1, anti-CTLA-4, or combination therapy. We developed the algorithm Cyclone to track temporal clonal dynamics and underlying cell states. Checkpoint blockade induced waves of clonal T cell responses that peaked at distinct timepoints. Combination therapy resulted in greater magnitude of clonal responses at 6 and 9 weeks compared to single-agent therapies, including melanoma-specific CD8 T cells and exhausted CD8 T cell (TEX) clones. Focused analyses of TEX identified that anti-CTLA-4 induced robust expansion and proliferation of progenitor TEX, which synergized with anti-PD-1 to reinvigorate TEX during combination therapy. These next generation immune profiling approaches can guide the selection of drugs, schedule, and dosing for novel combination strategies.

overall_design: We performed single-cell RNA sequencing on CD8+ and CD4+ T cells sorted from PBMCs and CD45+ cells sorted from tumor biopsies collected from 3 treatment-naïve patients with Stage III melanoma.

first: Wang

last: Kevin

first: Paulina

last: Coutifaris

first: Brocks

last: David

last: Guanning

first: Azar

last: Tarek

first: Solis

last: Sabrina

first: Nandi

last: Ajeya

first: Anderson

last: Shaneaka

first: Han

last: Nicholas

first: Manne

last: Sasikanth

first: Kiner

last: Evgeny

first: Sachar

last: Chirag

first: Lucas

last: Minke

first: George

last: Sangeeth

first: Yan

middle: K

last: Patrick

first: Kier

middle: W

last: Melanie

first: Laughlin

middle: I

last: Amy

first: Kothari

last: Shawn

first: Giles

last: Josephine

first: Mathew

last: Divij

first: Ghinnagow

last: Reem

first: Alanio

last: Cecile

first: Flowers

last: Ahron

first: Xu

last: Wei

first: Tenney

middle: J

last: Daniel

last: Xiaowei

first: Amaravadi

last: Ravi

first: Karakousis

last: Giorgos

first: Schuchter

middle: M

last: Lynn

first: Buggert

last: Marcus

first: Oldridge

last: Derek

first: Minn

last: Andy

first: Blank

last: Christian

first: Weber

middle: S

last: Jeffrey

first: Mitchell

last: Tara

first: Farwell

middle: D

last: Michael

first: Herati

last: Ramin

first: Huang

last: Alexander


title: GABAergic neuronal lineage development determines clinically actionable targets in diffuse hemispheric glioma, H3G34-mutant [ChIP-Seq]

city: Sutton

first: Chris

last: Jones

state: Surrey

address: 15 Cotswold Road

department: Molecular Pathology

country: United Kingdom

institute: Institute of Cancer Research

summary: Diffuse hemispheric gliomas, H3G34R/V-mutant (DHG-H3G34), are uniformly lethal malignancies lacking targeted therapies. These gliomas uniquely originate from interneuronal precursor cells, and leveraging this interneuronal lineage origin for mechanistic and therapeutic insights is a pressing need. Here, we elucidate the cell state composition of DHG-H3G34, resolving a cellular hierarchy along continuous interneuron lineage development.  In the developing human brain, interneuron lineage precursors form characteristic histological patterns organized in streams of progenitor cells surrounding nests of migratory interneurons, and we find these same spatial patterns to be mirrored in primary DHG-H3G34 tumors. We integrated these findings with genome-wide CRISPR-Cas9 screens, which revealed the majority of dependencies to be genes upregulated in interneuron lineage progenitors, highlighting these as a driver of DHG-H3G34. We validated the essentiality of these lineage-associated targets in patient-derived in vitro and in vivo models. Among these, CDK6 emerged as a targetable dependency, and we demonstrated enhanced sensitivity of DHG-H3G34 tumor cells to CDK4/6 inhibitors and a CDK6-specific degrader. Inhibition of CDK6 shifted cells towards more mature interneuron-like cell states, reduced tumor growth, and prolonged survival of patient-derived xenografts. Concordantly, a patient with progressive DHG-H3G34 under second line therapy was treated with a CDK4/6 inhibitor, and exhibited stable disease for 17 months. Collectively, we identify interneuronal progenitor-like states, organized in characteristic developmental spatial niches, as a distinct vulnerability consistently upregulated in DHG-H3G34 tumors, and provide initial evidence for CDK6 as a clinically actionable target particularly relevant for its interneuronal developmental biology.

overall_design: Ch-IP sequencing of of DHG-G34 patient derived glioma cells

first: Ilon

last: Liu

first: Gustavo

last: Alencastro Veiga Cruzeiro

first: Lynn

last: Bjerke

first: Rebecca

middle: F

last: Rogers

first: Yura

last: Grabovska

first: Alan

last: Mackay

first: Mariella

middle: G

last: Filbin


title: Oncogenic SLC2A11-MIF Fusion Protein Interacts with PTBP1 to Facilitate Bladder Cancer Proliferation and Metastasis by Regulating mRNA Stability

city: Guangzhou

first: Liang

last: Cheng

state: Guangdong

address: 107th Yanjiangxi Road

department: Department of Urology

institute: Sun Yat-sen Memorial Hospital

summary: To further identify the underlying mechanisms of SLC2A11-MIF in bladder cancer progress, we performed genome-wide RNA expression profile screening in which we compared gene expression profiles in SLC2A11-MIF-knockdown and control cells in T24 or UM-UC-3

overall_design: Bladder cancer cells T24 or UM-UC-3 were treated with SiRNA or control  for 48h, respectively. The RNA of the treated cells was extracted and sequenced on Illumina NovaseqTM 6000 platform and 150-bp paired-end reads were generated.

first: Hui

last: Li

first: Xu

last: Chen

first: Jian

last: Huang


title: GABAergic neuronal lineage development determines clinically actionable targets in diffuse hemispheric glioma, H3G34-mutant [RNA-Seq]

overall_design: Differential expression by RNASeq of DHG-G34 patient derived glioma cells to the inhibition of CDK6 using Abemaciclib, Ribociclib, shRNAi and tergeted CDK6 degraders


title: The gene expression of microglia in the brain after ischemic stroke

city: shanghai

first: wan

last: hanxi

state: 上海

address: shanghai

institute: tongji university

summary: In this study, we focused on microglia in the central nervous system and analyzed microglia in mouse models of tMCAO.

overall_design: To examine the tissue or disease specific gene expression of microglia in the brain after ischemic stroke, we performed bulk RNAseq of microglia of 6 different isolated microglia sample (each sample contain 30 mice).

first: Hanxi

last: wan

first: Chun

first: Mengfan

last: He

first: Kexin

last: Yang

first: Ji

last: Hu

first: Li

last: Tian

first: Lize

last: Xiong


title: Modulating the Extracellular Matrix to Treat Wound Healing Defects in Ehlers-Danlos Syndrome

city: Los Angeles

first: Kindra

last: Kelly-Scumpia

state: CA

address: 615 Charles E Young Dr Rm 246

institute: UCLA

summary: Classic Ehlers Danlos syndrome (cEDS) is one of the most common genetic disorders of the connective tissue and musculoskeletal system characterized by mutations in genes encoding for type V collagen. Defects in wound healing constitute one of the most common and debilitating symptoms in individuals with cEDS but currently, no therapeutic strategies exist to attenuate wound healing defects in cEDS. We create a new murine model of cEDS, that remarkably phenocopies wound healing defects in human cEDS. Using this model, we show that an abnormal extracellular matrix (ECM) characterized by fibrillar disarray, altered mechanical properties and decreased collagen deposition contribute to the wound healing defect in cEDS. The cEDS animals exhibit decreased expression of epidermal genes and increased inflammation consistent with the human phenotype. We show that integrin expression is altered in wounds of cEDS animals and small molecule modulators of mechanosensitive integrin signaling attenuate wound healing defects. Finally, we demonstrate that rescuing extracellular matrix defects by injecting wild type fibroblasts into wounds of cEDS animals significantly enhances epidermal gene expression, decreases inflammation, augments wound closure and rescues defective wound repair. Taken together, these observations suggest that modulation of the extracellular matrix in Ehlers-Danlos syndrome either with small molecule inhibitors of mechanosensitive integrin signaling, or direct injection of wild type fibroblasts into the wound bed may have therapeutic potential for enhancing wound healing in cEDS.

overall_design:
Examination of mouse skin cell expression changes after wounding in:
WT vs Col5a1 CKO at day 14 and day 19
WT vs Col5a1 CKO at day 14 with and without transfer of WT fibroblasts in Col5a1 CKO animals
WT+vehicle vs Col5a1 CKO+vehicle or Col5a1 CKO+ cilengitide at day 14 (cil_rnaseq2.txt)

first: K

first: Maaini

last: Archang

first: Prabhat

last: Purbey

first: Tomohiro

last: Yokota

first: Rimao

last: Wu

first: Jackie

last: McCourt

first: Shen

first: R

middle: H

last: Crosbie

first: P

middle: O

last: Scumpia

first: Arjun

last: Deb


title: Conserved dorsal horn neuron subtype-specific enhancers are implicated in the genetic risk of chronic pain [Macaque snRNA-seq]

city: Pittsburgh

first: Michael

last: Leone

address: 4315 Tesla St

institute: Carnegie Mellon University

summary: The dorsal horn of the spinal cord transforms incoming somatosensory information and transmits it supraspinally to generate sensory perception, including pain and itch. Recent research using mouse Cre-driver lines has implicated specific populations of dorsal horn neurons in the transmission of different types of pain. In parallel, human genome-wide association studies (GWAS) have identified dozens of loci confidently associated with the genetic predisposition to chronic pain. The ability to connect controlled experiments in rodent models with human genetic studies could provide a platform for translational research, but the cell type heterogeneity of the dorsal horn and the complex genetic architecture of chronic pain have created challenges in bridging that gap. Here, we apply a variety of single cell genomic technologies and a comparative genomic analysis to identify conserved dorsal horn neuron subtypes whose open chromatin regions show enrichment for genetic variants associated with human chronic pain phenotypes. To achieve this, we first use single nucleus RNA-Seq and fluorescence in situ hybridization in Rhesus macaque to create a more detailed map of primate dorsal horn neuron subtypes. These were integrated with publicly available human and mouse single nucleus RNA-Seq datasets to create a multi-modal cross species atlas. Then, for the mouse dorsal horn, we combined single nucleus RNA-Seq, spatial transcriptomics, and single nucleus ATAC-Seq to infer spatial and epigenomic profiles of conserved dorsal horn neuron subtypes. Finally, we compared our conserved cell-type open chromatin resource to chronic pain GWAS and found that open chromatin regions of specific dorsal horn neuron subtypes showed enrichment for a variety of human chronic pain phenotypes. Our results provide a foundation to further explore how conserved dorsal horn neuron subtypes influence the transmission of pain signals.

overall_design: Spinal cord dissections from healthy adult (n=3 M macaques), were taken to generate single nucleus suspensions for snRNA-seq

first: Cynthia

last: Arokiaraj

first: Rebecca

middle: P

last: Seal

first: Andreas

middle: R

last: Pfenning


title: Conserved dorsal horn neuron subtype-specific enhancers are implicated in the genetic risk of chronic pain [Mouse snATAC-seq]

overall_design: Spinal cord dissections from healthy adult (n=20 F/M mice), were taken to generate single nucleus suspensions for snATAC-seq.


title: Conserved dorsal horn neuron subtype-specific enhancers are implicated in the genetic risk of chronic pain [Mouse Xenium]

overall_design: Spinal cord dissections were taken from two healthy mice that underwent sterile saline injection (mouse 1, Male) or naive brush (mouse 2, Female) for the Xenium spatial transcriptomics assay using the 2023 mouse brain panel of 148 genes.


title: JAK-STAT1 as therapeutic target for EGFR deficiency-associated inflammation and scarring alopecia (scRNA-seq)

status: Public on Jul 31 2024

city: Vienna

first: Thomas

last: Bauer

state: Vienna

address: Borschkegasse 8A

department: Center for Cancer Research

country: Austria

institute: Medical University of Vienna

summary: The hair follicle stem cell niche is an immune-privileged microenvironment, characterized by reduced antigen presentation, thus shielding against permanent immune-mediated tissue damage. In this study, we demonstrated the protective role of hair follicle-specific epidermal growth factor receptor (EGFR) against scarring hair follicle destruction. Mechanistically, disruption of EGFR signalling generated a cell-intrinsic hypersensitivity within the JAK-STAT1 pathway, which, synergistically with interferon gamma expressing CD8 T-cell and NK-cell-mediated inflammation, compromised the stem cell niche. Hair follicle-specific genetic depletion of either JAK1/2 or STAT1 or therapeutic inhibition of JAK1/2 ameliorated the inflammation, restored skin barrier function and activated the residual stem cells to resume hair growth in mouse models of epidermal and hair follicle-specific EGFR deletion. Skin biopsies from EGFR inhibitor-treated and cicatricial alopecia patients indicated active STAT1 signalling and interferon target expression. Notably, a case study of folliculitis decalvans, characterized by progressive hair loss, scaling and perifollicular erythema, demonstrated successful treatment with JAK1/2 inhibition. Our findings offer molecular insights and present a mechanism-based therapeutic strategy for addressing chronic folliculitis associated with EGFR-inhibitor anti-cancer therapy and cicatricial alopecia.

overall_design: In order to expand the depth of the immunological analysis, we performed single-cell RNA sequencing of the hair follicle and immune cell compartment of 4 EGFRdeltaEgr2 mice at 3 months of age.

first: Karoline

last: Strobl

first: Regina

last: Jin


title: Epigenetic memory of radiotherapy in dermal fibroblasts impairs wound repair capacity in cancer survivors (ATAC-Seq)

first: Ning

last: Xu Landén

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: ATAC-seq was conducted on human skin fibroblasts isolated from both previously irradiated and non-irradiated areas of the same cancer patient, aiming to identify open chromatin regions across the genome. ATAC-seq was performed on human skin dermal fibroblasts treated with and without in vitro irradiation to identify open chromatin regions across the genome. ATAC-seq was performed on mouse dermal cells or fibroblasts isolated from irradiated or non-irradiated mice to identify open chromatin regions across the genome.

first: Xiaowei

last: Bian

first: Minna

last: Piipponen

first: Zhuang

last: Liu

first: Lihua

last: Luo

last: Landén


title: JAK-STAT1 as therapeutic target for EGFR deficiency-associated inflammation and scarring alopecia (RNA-seq of HFSC)

overall_design: To analyze the transcriptional status of hair follicle stem cells (HFSC) at 1 month, we isolated these cells using the CD34 HFSC surface marker from 3 WT and 3 EGFRdeltaEgr2 mice and performed RNA sequencing.


title: Conserved dorsal horn neuron subtype-specific enhancers are implicated in the genetic risk of chronic pain.

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

sample_organism:
Macaca mulatta
Mus musculus

platform_organism:
Macaca mulatta
Mus musculus

overall_design: Refer to individual Series


title: Transcriptome profiling associated with CARD11 overexpression in Colorectal Cancer implicates a potential role for Tumour Immune Microenvironment and Cancer pathways modulation via NF-κB

city: Sharjah

first: Rifat

last: Hamoudi

state: Sharjah

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

department: Clinical Sciences

country: United Arab Emirates

institute: University of Sharjah

summary: The immune system plays a critical role in inflammation by initiating responses to infection or tissue damage. NF-κB pathway plays a key role in inflammation and innate immunity, as well as other cellular activities. Furthermore, dysregulation of this well-choreographed pathway has been observed in many diseases, including cancer. CARD11 is a key molecule in the BCL-10, MALT1 (CBM) complex which is involved in transducing the signal downstream of the NF-κB pathway. This study aims to understand how overexpression of CARD11 adversely affects the prognosis in colorectal cancer (CRC) as it progresses towards aggressive form of the disease and the role that CARD11 plays in modulating the immune response across the different stages of CRC. To identify some of the cellular pathways activated as a result of CARD11, whole tran-scriptomics analysis was carried comparing the transcriptomic profile of CARD11-overexpressed HCT-116 and HT-29 CRC cell lines with empty vector-transfected cell lines as well as comparing adenoma and carcinoma CRC patients with CARD11- and CARD11+ expression. The whole tran-scriptomics and bioinformatics analysis results strongly suggested that CARD11 appears to play a key role in CRC progression. Absolute Gene Set Enrichment Analysis (absGSEA) on HCT-116 transcriptomics data showed that CARD11 overexpression promotes cell growth, and tissue re-modeling as well as enhancing the cell’s immune response. Some of the underlying genes in-volved in such processes through co-expression with CARD11 include EP300, KDM5A, HIF1A, NFKBIZ, and DUSP1. Results for HT-29 showed that CARD11 overexpression induces chemotaxis and ECM organization pathways through co-expression of IL1RN, MDK, and SPP1 as well as var-ious chemokines including CXCL1, CXCL3 and CCL22 which were shown to contribute to the more invasive stage of CRC. For patients, the adenoma patients include genes related to tumour immune microenvironment such as IL6ST, genes related to collagen family as well as other genes related to transition to CRC such as GLI3 and PIEZO2. While carcinoma patients show dramatic increase in the expression of MAPK8IP2 in CARD11+ carcinoma patients in addition to other genes related to cancer processes including EMB, EPHB6, and CPEB4. Taken together, the results show that CARD11 overexpression contributes to the progression of CRC through modu-lation of various tumour immune microenvironment pathways and activation of cancer path-ways possibly via the dysregulation of NF-κB. To our knowledge, this is probably the first study that investigates the role of CARD11 in CRC and the genes and pathways associated with CARD11 overexpression may provide insights into the early diagnostic and possible therapeutic targets for CRC.

overall_design:
In order to understand how dysregulation of CARD11 adversely affects the prognosis in CRC as it progresses towards an aggressive form (or how does CARD11 links to the poor prognosis) and modulates the immune response in different stages of CRC and worsens the prognosis, RNAseq and bioinformatics analysis were conducted in CARD11-overexpressed HCT116 and HT29 CRC cell lines as well as in patients with adenoma and carcinoma CRC either CARD11- or CARD11+ expression.
Empty vector transfected HCT116 or HT29 cell lines were used as control, and CARD11 transfected HCT116 and HT29 cell lines for overexpression studies.
10 adenoma and 13 carcinoma FFPE tissue samples were used. Among 10 adenoma patients, four samples were identified as low CARD11 expression (CARD11-) and six samples were identified as high CARD11 expression (CARD11+), whereas in 13 carcinoma samples eight samples were identified as low CARD11 expression (CARD11-) and five samples were identified as high CARD11 expression (CARD11+).
Abbreviations: (AD: Adenoma patients, CA: Carcinoma patients)

first: Faisal

last: Mohamed Alhosani

first: Burcu

last: Yener Ilce

first: Reem

last: Sami Alhamidi

first: Poorna

last: Manasa Bhamidimarri

first: Alaa

last: Hamad Mohamed

first: Noura

last: Alkhayyal

first: Kadria

last: Sayed

first: Axel

last: Kunstner

first: Hauke

last: Busch

first: Ali

last: Al Fazari

first: Riyad

last: Bendardaf

first: Basel

last: Al-Ramadi

first: Cyrus

last: Khandanpour

middle: A


title: AS01-adjuvanted vaccine promotes functional and epigenetic modifications in monocytes [Nanostring panel]

city: Rixensart

first: Viviane

middle: Jeanne

last: Bechtold

state: Brabant Wallon

address: rue de l'Institut 89

department: Molecular Biology

country: Belgium

institute: GSK

summary: HBS/AS01 adjuvanted vaccine induces changes in the chromatin structure of monocytes after vaccination, an effect that lasts until 6 months post vaccination

overall_design:
frozen PBMCS isolated at D32, D44, D60, D180 post dose 2 after HBS/AS01 vaccination were depleted of CD3+ cells and processed via nanostring
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Submitter states that missing raw files are due to patient privacy concerns.
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first: Benoit

last: Bozzetti

first: Laurie

last: Dumont


title: Leveraging deep single-soma RNA sequencing to explore the neural basis of human somatosensation

first: Huasheng

last: Yu

state: PENNSYLVANIA

address: 3610 Hamilton Walk

department: Neuroscience

summary: The versatility of somatosensation arises from heterogeneous dorsal root ganglion (DRG) neurons. However, soma transcriptomes of individual human (h)DRG neurons-critical information to decipher their functions-are lacking due to technical difficulties. In this study, we isolated somata from individual hDRG neurons and conducted deep RNA sequencing (RNA-seq) to detect, on average, over 9,000 unique genes per neuron, and we identified 16 neuronal types. These results were corroborated and validated by spatial transcriptomics and RNAscope in situ hybridization. Cross-species analyses revealed divergence among potential pain-sensing neurons and the likely existence of human-specific neuronal types. Molecular-profile-informed microneurography recordings revealed temperature-sensing properties across human sensory afferent types. In summary, by employing single-soma deep RNA-seq and spatial transcriptomics, we generated an hDRG neuron atlas, which provides insights into human somatosensory physiology and serves as a foundation for translational work.

overall_design: Single cell transcriptomic study of human sensory DRG neurons. This dataset includes 1136 cells from three individuals using the laser capture microdissection combined with Smart-seq2 protocol.

first: Dmitry

last: Usoskin

first: Saad

last: Nagi

first: Yizhou

last: Hu

first: Jussi

last: Kupari

first: Otmane

last: Bouchatta

first: Suna

middle: L

last: Cranfill

first: Mayank

last: Gautam

first: Yijing

last: Su

first: You

last: Lu

first: James

last: Wymer

first: Max

last: Glanz

first: Phillip

last: Albrecht

first: Hongjun

last: Song

first: Guo-Li

last: Ming

first: Stephen

last: Prouty

first: John

last: Seykora

first: Hao

last: Wu

first: Minghong

last: Ma

first: Frank

last: Rice

first: Håkan

last: Olausson

first: Patrik

last: Ernfors

first: Wenqin

last: Luo


title: Multi-omics analysis of longitudinal patient samples reveals the molecular mechanism of AML progression [ATAC-seq]

city: Old Al rayyan

first: Nisar

last: Ahmed

state: Doha

address: LAS Building, Education city

department: College of Health and Life Sciences

country: Qatar

institute: Hamad Bin Khalifa University

summary: Relapse remains a determinant of treatment failure and contributes significantly to mortality in acute myeloid leukemia (AML) patients. Despite efforts to understand AML progression and relapse mechanisms, findings on acquired gene mutations in relapse vary, suggesting inherent genetic heterogeneity and emphasizing the role of epigenetic modifications. Herein, we characterized genetic and epigenetic changes in AML progression using multi-omics approaches to elucidate the underlying mechanisms of relapse. Differential interaction analysis showed significant 3D chromatin landscape reorganization between relapse and diagnosis samples. Comparing global open chromatin profiles revealed that relapse samples had significantly fewer accessible chromatin regions than diagnosis samples. In addition, we discovered that relapse-related upregulation was achieved either by forming new active enhancer contacts or by losing interactions with poised enhancers/potential silencers. Altogether, our study highlights the impact of genetic and epigenetic changes on AML progression, underlining the importance of multi-omics approaches in understanding disease relapse mechanisms and guiding potential therapeutic interventions.

overall_design: We conducted a multi-omics analysis using Omni-C, ATAC-seq, and RNA-seq on longitudinal samples from two adult AML patients at diagnosis and relapse.

first: Chiara

last: Cugno

first: Sara

last: Deola

first: Borbala

last: Mifsud


title: AS01-adjuvanted vaccine promotes functional and epigenetic modifications in monocytes [scATAC-seq]

first: Viviane

last: Bechtold

summary: HBS/AS01 adjuvanted vaccine induces changes in the chromatin structure in monocyte population impacting their gene expression, an effect that lasts until 6 months post vaccination

overall_design:
frozen PBMCS isolated at D32, D44, D60, D180 post dose 2 after HBS/AS01 vaccination were depleted from CD3+ cells and processed via single cell ATACseq

***************************************************************
Submitter states that missing raw files are due to patient privacy concerns.
***************************************************************

first: Ahmed

last: Essaghir

first: Aline

last: Scaillet

first: Stephanie

last: Tilman

first: Benoit

last: Bozzetti


title: AS01-adjuvanted vaccine promotes functional and epigenetic modifications in monocytes


title: snRNA-Seq from Younger and Older human abdominal subcutaneous white adipose tissue

city: Orlando

first: Lauren

last: Sparks

state: Florida

address: 301 E Princeton St, 301

institute: AdventHealth

summary:
Abstract
White adipose tissue (WAT) is a robust energy storage and endocrine organ critical for maintaining metabolic health as we age. Our aim was to identify cell-specific transcriptional aberrations that occur in WAT with aging. We leveraged full-length snRNA-Seq and histology to characterize the cellular landscape of human abdominal subcutaneous WAT in a prospective cohort of 10 younger (≤30 years) and 10 older individuals (≥65 years) balanced for sex and body mass index (BMI). The older group had greater cholesterol, very-low-density lipoprotein, triglycerides, thyroid stimulating hormone, and aspartate transaminase compared to the younger group (p< 0.05). We highlight that aging WAT is associated with adipocyte hypertrophy, increased proportions of lipid-associated macrophages and mast cells, an upregulation of immune responses linked to fibrosis in pre-adipocyte, adipocyte, and vascular populations, and highlight CXCL14 as a biomarker of these processes. We show that older WAT has elevated levels of senescence marker p16 in adipocytes and identify the adipocyte subpopulation driving this senescence profile. We confirm that these transcriptional and phenotypical changes occur without overt fibrosis and in older individuals that have comparable WAT insulin sensitivity to the younger individuals.

overall_design:
snRNA-Seq on frozen abdominal subcutaneuous white adipose tissue from 10 Younger and 10 Older individuals (as listed in the README.txt).
Please note that as two individual samples were sequenced on the same paired-end lane (i.e. each pair of FASTQ files belongs to two samples), mixed sample records have been created.

first: L


title: AS01-adjuvanted vaccine promotes functional and epigenetic modifications in monocytes [RNA-seq]

summary: HBS/AS01 adjuvanted vaccine induces changes in the chromatin structure in monocytes impacting their gene expression profiles, an effect that lasts until 6 months post vaccination

overall_design:
CD14+ monocytes were isolated from frozen PBMCs at different time points post vaccination to monitor their gene expression profiles

***************************************************************
Submitter states that missing raw files are due to patient privacy concerns.
***************************************************************

first: Stépahnie


title: AS01-adjuvanted vaccine promotes functional and epigenetic modifications in monocytes [scRNA-seq]

overall_design:
frozen PBMCS isolated at D32, D44, D60, D180 post dose 2 after HBS/AS01 vaccination were depleted from CD3+ cells and processed via single cell RNAseq

***************************************************************
Submitter states that missing raw files are due to patient privacy concerns.
***************************************************************


title: Multi-omics analysis of longitudinal patient samples reveals the molecular mechanism of AML progression [Omni-C]


title: DNA Methylomic Differences in Adults Asthmatics of Varying Severity and Exposure to Air Pollution

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

summary: Rationale: DNA methylation plays a critical role in asthma development, but differences in DNA methylation associated with asthma severity, especially among adults, are less well-defined. Changes in DNA methylation are influenced by exposure to air pollution, which is a risk factor for asthma exacerbation and severity. Here, we examined how DNA methylomic patterns in adult asthmatics differ by asthma severity and exposure to different components of air pollution. Methods: Peripheral blood CD3+ T cells from adult asthmatics in Beijing, China were serially collected from 37 patients (130 samples total) and analyzed for global DNA methylation using the Illumina MethylationEPIC Array. Measurements and Main Results: Significant differences in DNA methylation were noted among subjects with different degrees of asthma severity, as measured by fraction of exhaled nitric oxide, forced expiratory volume, and asthma control test scores. Differences in DNA methylation were annotated to genes that were enriched in pathways related to asthma or T cell function, and included gene ontology categories related to cellular adhesion, developmental pathways, and calcium signaling. Notable genes that were differentially methylated based on asthma severity included RUNX3, several members of the HLA family, PDGFRA, CDH1, CAV1, and NOTCH4. Differences in DNA methylation also varied by exposure to ambient air pollution, with different components of pollution effecting methylation of different groups of genes. Conclusion: These findings demonstrate how adult asthmatics possess widespread differences in the DNA methylation that associated with varying asthma severity and how air pollution might contribute to more severe asthma via changes in DNA methylation.

overall_design: Blood samples were collected at baseline (0), 3 months (V3), 6 months (V6), 9 months (V9), and 12 months (V12) from 37 adults in Beijing, China with a clinical diagnosis of asthma. CD3+ T cells were isolated from blood samples using anti-CD3 magnetic particles and DNA was extracted from these cells using the QlAmp DNA Micro Kit before bisulfite conversion and analysis on the Illumina Infinium MethylationEPIC BeadChip array. Clinical data including lung function, fraction of exhaled nitric oxide, and asthma control test results were collected at the time of blood sample collection and changes in methylation were correlated with clinical parameters of asthma. Sample number indicates different subject IDs.

first: Steven

last: Huang

first: Yahong

last: Chen


title: ANGPTL4 suppress clear cell renal cell carcinoma via inhibition lysosomal acid lipase

status: Public on Jul 30 2024

city: Gainesville

first: Ryan

last: Kolb

state: FL

address: 1275 Center Drive, M656

department: Pathology, Immunology and Laboratory Medicine

institute: University of Florida

summary: Renal cell carcinoma (RCC), the most common form of kidney cancer, is a heterogeneous disease with clear cell RCC (ccRCC) being the most prevalent and aggressive subtype. While most ccRCC tumors have elevated expression of angiopoietin-like 4 (ANGPTL4), in our study we identified a significant subset of patients whose cancers show no increase in ANGPTL4 expression. These patients have a worse prognosis compared to the patients with high expression of ANGPTL4. These ANGPTL4-low cancers are characterized by the increased frequency of wild-type Von Hippel-Lindau (wt VHL), a gene that is commonly mutated in ccRCC, and an enrichment for genes associated with lipid metabolism. Using RCC tumor models with wild type VHL, we demonstrate that ANGPTL4 behaves as a tumor suppressor. The loss of ANGPTL4 in ccRCC cell lines results in increased tumor growth and colony formation in a lysosomal acid lipase (LAL)-dependent manner, a phenotype rescued by the expression of N-terminus ANGPTL4. At the mechanistic level, the loss of ANGPTL4 increases lysosomal acid lipase activity in ccRCC cells. This data suggests that ANGPTL4 enacts its tumor-suppressive effects in ccRCC by regulating LAL activity. Importantly, the identified patient cohort with low ANGPTL4 expression may exhibit increased reliance on lipid metabolism, which can be a point of target for future therapy.

overall_design: To investigate transcriptional changes as a result of loss of ANGPTL4. Human ccRCC cell lines, 786O and CAKi-1, were directly transfected with Caspase 9 protein and a single guide RNA for ANGPTL4 to generation pools of knockouit cells. Single clones were grown and clones with loss of ANGPTL4 mRNA were combined to generate ANGPTL4 knockout (KO)( cells. Clones without loss of ANGPTL4 were combined to gnerate wild type (WT) cells. Comparative gene expression profiling was perfromed from RNAseq of 4 WT and 5 KO CAKI-1 replicates and 3 WT and 3 KO 786O replicates.

first: Zeng

last: Jin


title: Combination anti-PD-1 and anti-CTLA-4 therapy generates waves of clonal responses that include progenitor-exhausted CD8 T cells [dataset 3]

first: Alexander

middle: C

summary: Combination checkpoint blockade with anti-PD-1 and anti-CTLA-4 antibodies has shown promising efficacy in melanoma. However, the underlying mechanism in humans remains unclear. We performed RNA+TCR single-cell analysis across time in 36 stage IV melanoma patients treated with anti-PD-1, anti-CTLA-4, or combination therapy. We developed the algorithm Cyclone to track temporal clonal dynamics and underlying cell states. Checkpoint blockade induced waves of clonal T cell responses that peaked at distinct timepoints. Combination therapy resulted in greater magnitude of clonal responses at 6 and 9 weeks compared to single-agent therapies, including melanoma-specific CD8 T cells and exhausted CD8 T cell (TEX) clones. Focused analyses of TEX identified that anti-CTLA-4 induced robust expansion and proliferation of progenitor TEX, which synergized with anti-PD-1 to reinvigorate TEX during combination therapy. These next generation immune profiling approaches can guide the selection of drugs, schedule, and dosing for novel combination strategies.

overall_design: We performed single-cell RNA+TCR sequencing on CD8 T cells sorted from PBMCs collected 3 weeks apart from two healthy donors.

first: Wang

last: Kevin

first: Paulina

last: Coutifaris

first: Brocks

last: David

last: Guanning

first: Azar

last: Tarek

first: Solis

last: Sabrina

first: Nandi

last: Ajeya

first: Anderson

last: Shaneaka

first: Han

last: Nicholas

first: Manne

last: Sasikanth

first: Kiner

last: Evgeny

first: Sachar

last: Chirag

first: Lucas

last: Minke

first: George

last: Sangeeth

first: Yan

last: Patrick

first: Kier

last: Melanie

first: Laughlin

last: Amy

first: Kothari

last: Shawn

first: Giles

last: Josephine

first: Mathew

last: Divij

first: Ghinnagow

last: Reem

first: Alanio

last: Cecile

first: Flowers

last: Ahron

first: Xu

last: Wei

first: Tenney

last: Daniel

last: Xiaowei

first: Amaravadi

last: Ravi

first: Karakousis

last: Giorgos

first: Schuchter

last: Lynn

first: Buggert

last: Marcus

first: Oldridge

last: Derek

first: Minn

last: Andy

first: Blank

last: Christian

first: Weber

last: Jeffrey

first: Mitchell

last: Tara

first: Farwell

last: Michael

first: Herati

last: Ramin

first: Huang

last: Alexander


title: SDePER: a hybrid machine learning and regression method for cell-type deconvolution of spatial barcoding-based transcriptomic data

city: New Haven

first: Naftali

last: Kaminski

state: CT

address: 300 Cedar Street

institute: Yale University

summary: Spatial barcoding-based transcriptomic (ST) data require cell type deconvolution for cellular-level downstream analysis. Here we present SDePER, a hybrid machine learning and regression method, to deconvolve ST data using reference single-cell RNA sequencing (scRNA-seq) data. SDePER removes the systematic difference between the ST and scRNA-seq data (platform effects) explicitly and efficiently to ensure the linear relationship between ST data and cell type-specific expression profile. It also considers sparsity of cell types per capture spot and across-spots spatial correlation in cell type compositions. Based on the estimations, SDePER imputes for cell type compositions and gene expression at enhanced resolution. We assessed the performance of SDePER and six existing methods using simulations and four real datasets. All results showed that SDePER achieved significantly more accurate and robust results than the existing methods suggesting the importance of considering platform effects, sparsity and spatial correlation in cell type deconvolution.

overall_design: We measured the ST data of a human IPF lung using the 10x Genomics Visium platform to identify the transcriptome of different lung compartments including the bronchi, vascular, mesenchyme and immune compartment. Samples were obtained from explanted lung. We selected one block of frozen lung tissue obtained from a patient with Idiopathic Pulmonary Fibrosis (IPF). Sections of 10 μm (fresh frozen samples) were cut from the blocks onto Visium slides (10X Genomics) and processed according to the manufacturer’s protocol Tissue sections were Hematoxylin and Eosin stained and finally imaged (20X) using a scanning microscope (EvosM700, ThermoFischer Scientific). Tissue was permeabilized and mRNAs were hybridized to the barcoded capture probes directly underneath. cDNA synthesis connects the spatial barcode and the captured mRNA. After RT and amplification by PCR, Dual-indexed libraries were prepared as in the 10X Genomics protocol, and sequenced (2 samples/ HiSeq 6000 flow cell) with read lengths 28 bp R1, 10 bp i7 index, 10 bp i5 index, 90 bp R2.

first: Aurelien

last: Justet

first: Taylor

last: Adams

first: Agshin

last: Balayev

first: Thomas

last: Barnthaler

first: Fernando

last: Poli de Frias

first: Juan

last: Cala-Garcia

first: John

last: McDonough

first: Jasper

last: Flint

first: Jonas

last: Schupp

first: Amy

last: Zhao

first: Joe

last: Deluliis

first: Yunqing

last: Liu

first: Ningshan

last: Li

first: Sam

last: Raredon

first: Anita

last: Wang

first: Adan

last: Lepe

first: Neba

last: Abu Husseinl

first: Farida

last: Ahangari

first: Xiting

last: Yan

first: Ivan

last: Rosas


title: Combination anti-PD-1 and anti-CTLA-4 therapy generates waves of clonal responses that include progenitor-exhausted CD8 T cells [dataset 2]

first: Alexander

last: Huang

overall_design: For this dataset, we performed single-cell RNA+TCR sequencing on CD8 T cells sorted from PBMCs collected from 4 melanoma patients at baseline and every 3 weeks after anti-PD-1 checkpoint blockade.

first: Wang

last: Kevin

first: Paulina

last: Coutifaris

first: Brocks

last: David

last: Guanning

first: Azar

last: Tarek

first: Solis

last: Sabrina

first: Nandi

last: Ajeya

first: Anderson

last: Shaneaka

first: Han

last: Nicholas

first: Manne

last: Sasikanth

first: Kiner

last: Evgeny

first: Sachar

last: Chirag

first: Lucas

last: Minke

first: George

last: Sangeeth

first: Yan

middle: K

last: Patrick

first: Kier

last: Melanie

first: Laughlin

last: Amy

first: Kothari

last: Shawn

first: Giles

last: Josephine

first: Mathew

last: Divij

first: Ghinnagow

last: Reem

first: Alanio

last: Cecile

first: Flowers

last: Ahron

first: Xu

last: Wei

first: Tenney

last: Daniel

last: Xiaowei

first: Amaravadi

last: Ravi

first: Karakousis

last: Giorgos

first: Schuchter

last: Lynn

first: Buggert

last: Marcus

first: Oldridge

last: Derek

first: Minn

last: Andy

first: Blank

last: Christian

first: Weber

last: Jeffrey

first: Mitchell

last: Tara

first: Farwell

last: Michael

first: Herati

last: Ramin

first: Huang

last: Alexander


title: RNA sequensing data of a phase 2 clinical trial of pancreatic ductal adenocarcinoma treated with entinostat in combination with nivolumab

status: Public on Jul 29 2024

city: Baltimore

first: Ludmila

last: Danilova

address: 550 N Broadway St 1103E

institute: Johns Hopkins School of Medicine

summary: We conducted a single-center, open-label, Simon two-stage, phase II study of entinostat in combination with the PD1 inhibitor nivolumab in patients with advanced pancreatic ductal adenocarcinoma. Patients received oral entinostat 5 mg once a week. After a 14-day lead-in with entinostat monotherapy, patients concurrently receive entinostat 5 mg orally once a week plus nivolumab 240 mg intravenously until the time of progression or unacceptable toxicities.

overall_design: All patients underwent fresh tumor biopsy (subsequent passes flash frozen, formalin-fixed paraffin-embedded, and preserved in RNAlater) at baseline, after two weeks of entinostat lead-in therapy (C1D1), and on week 6 following entinostat given with nivolumab combination therapy (C2D1). The patient data and raw sequencing files are submitted to dbGaP: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs003615.v1.p1.

first: Marina

last: Baretti

first: Nilofer

last: Azad


title: Inhibition of miR-497-5p improves keratinocyte function upon skin exposure to sulfur mustard

status: Public on Jul 27 2024

city: Munich

first: Virginia

last: Egea

state: Bayern

address: Max-Lebsche Platz 30

department: IPEK

institute: LMU

type: Non-coding RNA profiling by high throughput sequencing

summary: Sulfur mustard (SM) is a hazardous chemical warfare agent. Exposure to SM results in various pathologies including skin lesions and impaired wound healing. To date, there are no effective treatments available. Here we discover that the miRNA miR-497-5p is induced in epidermal cells by SM and mediates keratinocyte dysfunction. Transcriptome analysis using RNA-seq in normal human epidermal keratinocytes (NHEK) revealed that SM evoked differential expression of 1,896 mRNAs and 25 miRNAs with many of these RNAs known to be involved in keratinocyte function and wound healing. We demonstrated that keratinocyte differentiation and proliferation were efficiently regulated by miRNAs induced in skin cells after exposure to SM. The inhibition of miR-497-5p counteracted SM-induced premature differentiation and inhibition of proliferation in NHEK. In addition, we showed that microneedle-mediated transdermal application of lipid-nanoparticles containing miR-497-5p inhibitor improved the healing of human skin biopsies upon exposure to SM. Our findings expand the current understanding of SM-associated molecular toxicology in keratinocytes and highlight miR-497-5p as feasible clinical target for specific skin therapy in SM-exposed patients and beyond.

overall_design: Normal human epidermal keratinocytes (NHEK) were left untreated or exposed to sulfur mustard (SM) at 10 µM and 30 µM or vehicle control (ethanol) (n = 4). After 24 hours of cultivation, mRNA and miRNA were isolated and subjected to RNA-seq analysis.

first: Helmut

last: Blum

first: Sarah

last: Reschke

first: Sajjad

last: Khani

first: Christian

last: Ries


title: Single nuclei ATACseq profiling of Human Pancreatic Islets across sex

status: Public on Jul 25 2024

city: New Orleans

first: Franck

last: Mauvais-Jarvis

state: LA

address: 1430 Tulane Avenue Lab# 2301

department: Department of Medicine - Section of Endocrinology and Metabolism

institute: Tulane University

summary: Mechanisms driving sex differences across islet cells is unknown. Thus, studying sex differences in islet regulation and function represent a unique avenue to understand the sex-specific heterogeneity in β cell failure in diabetes. We examined sex and race differences in human pancreatic islets from 15 donors using an orthogonal series of experiments including single cell RNA-seq (scRNA-seq), single nucleus assay for transposase-accessible chromatin sequencing (snATAC-seq), dynamic hormone secretion, and bioenergetics.

overall_design: Human islets (500 IEQ per condition) were cultured overnight in a humidified incubator containing 5% CO2 at 37°C. Islet cells were then dispersed using TrypLE (Thermofischer), and immediately evaluated for viability (90.61±3.04%) by Cellometer Automated Cell Counter (Nexcelom Bioscience) prior to single nuclei ATAC library preparation. Nuclei were isolated based on the 10X genomics Nuclei isolation protocol (CG00169 Rev D) with some modifications. We observe that the usage of 0.5ml tubes yields superior nuclei collection. Furthermore, we optimize based on a sample-to-sample basis the time for cell lysis (3-5min). The final lysis buffer concentration for Nonidet P40 was 0.15% over the 0.1% recommendation. Finally, in addition to the final wash with wash buffer, we perform a final wash with the 10X Genomics Nuclei Buffer (PN-2000153/2000207). Nuclei are always kept < 0°C, visually inspected for integrity and quality using a viability dye, prior to library prep which was performed within 30min. Briefly, 5,000-6,500 isolated nuclei were incubated with a transposition mix to preferentially fragment and tag the DNA in open regions of the chromatin. The transposed nuclei were then partitioned into nanoliter-scale Gel Bead-In-emulsions (GEMs) with barcoded gel beads, a master mix, and partition oil on a chromium chip H. Upon GEM formation and PCR, 10x barcoded DNA fragments were generated with an Illumina P5 sequence, a 16nt 10x barcode, and a read 1 sequence. Following library construction, sequencing-ready libraries were generated with addition of P7, a sample index, and a read 2 sequence. Quality controls of these resulting single cell ATAC libraries were performed by using Agilent High Sensitive DNA kit with Agilent 2100 Bioanalyzer (Agilent) and quantified by Qubit 2.0 fluorometer (ThermoFisher). Pooled libraries at a final concentration of 750pM were sequenced with paired-end dual indexing configuration by Illumina NextSeq 2000 (Illumina) to achieve 40,000-30,000 read pairs per nucleus.

first: Mirza

last: Qadir


title: Two-factor authentication underpins the precision of piRNA-directed LINE1 DNA methylation

status: Public on Jul 26 2024

city: Edinburgh

first: Madeleine

last: Heep

address: 5 Little France Drive

department: MRC Centre for Regenerative Medicine

institute: University of Edinburgh

summary: The PIWI-interacting RNA (piRNA) pathway guides the DNA methylation of young active transposons during male mouse germline development. piRNAs tether the PIWI protein MIWI2 (PIWIL4) to the nascent transposon transcript that results in DNA methylation through SPOCD1. Transposon methylation requires exacting precision: all copies need to be methylated yet, at the same time, off-target methylation must be avoided. However, the underlying mechanisms that ensure this precision remain unknown. Here, we show that SPOCD1 directly interacts with SPIN1, a chromatin reader that primarily binds H3K4me3 and this association is augmented by H3K9me3. The prevailing assumption is that all molecular events required for piRNA-directed DNA methylation occur after the engagement of MIWI2. Interestingly, we find that SPIN1 expression precedes that of both SPOCD1 and MIWI2. Furthermore, we demonstrate that young LINE1s, but not old copies are marked by H3K4me3 and H3K9me3 prior to the initiation of piRNA-directed DNA methylation. We generated a Spocd1 separation-of-function allele in the mouse that encodes a SPOCD1 variant that no longer interacts with SPIN1. We found that the SPOCD1-SPIN1 interaction is essential for spermatogenesis and piRNA-directed DNA methylation of young LINE1 elements. We propose that young LINE1 elements require a two-factor authentication process for DNA methylation, the first being the recruitment of SPIN1-SPOCD1 to licence the locus and the second is MIWI2 engagement with the nascent transcript, which is the trigger for methylation. In summary, independent events that licence, and trigger methylation underpin the basis of precision.

overall_design: Examination of RNA expression profiles in control (wildtype) and Spocd1 dSpin1/dSpin1 P20 testis.

first: Yuka

last: Kabayama

first: Tamoghna

last: Chowdhury

first: Ansgar

last: Zoch

first: Dónal

last: O'Carroll


title: TET2 regulates histone H2AK119ub and leukemogenesis through LTR RNA m5C oxidation [seq_RNA-totalRNA]

city: Shanghai

first: Xiaoyang

last: Dou

address: 320 Yue Yang Road

institute: CAS Center for Excellence in Molecular Cell Science, CAS

summary: Mutation of TET2 drives myeloid malignancy progression. TET2 deficiency is known to cause a globally opened chromatin and activation of genes contributing to aberrant HSPC self-renewal. We show here that chromatin-associated retrotransposon RNA 5-methylcytosine (m5C), installed by NSUN2, can be recognized by the methyl-CpG-binding domain protein MBD6, which guides deubiquitylation of nearby histone H2AK119ub to promote an open chromatin state. TET2 oxidizes m5C and antagonizes this MBD6-dependent H2AK119ub deubiquitylation. Thereby, TET2 depletion leads to globally decreased H2AK119ub, more open chromatin, and increased transcription in stem cells. TET2 mutant human leukemia became dependent on this gene activation pathway, with MBD6 silencing selectively inhibits proliferation of TET2 mutant leukemia in vitro and in vivo. Altogether, our findings reveal a previously unknown chromatin regulation pathway by TET2 through retrotransposon RNA m5C oxidation and identify the downstream MBD6 protein as a feasible target for developing therapies specific against TET2 mutant malignancies.

overall_design: Total RNA-seq in mouse LK cells and mRNA-seq in K562 cells

first: Zhongyu

last: Zou

first: Chuan

last: He


title: TET2 regulates histone H2AK119ub and leukemogenesis through LTR RNA m5C oxidation [seq_RNA-CLIP]

overall_design: MBD5 and MBD6 CLIP-seq in mESCs


title: Identifying regulatory variants using multiome single-cell sequencing in prostate cell lines

city: TAMPA

first: Liang

last: Wang

address: 14059 Riveredge Drove

institute: Moffitt Cancer Center

summary: Despite significant progresses, the genetic roles of regulatory elements in gene expression still remain largely unknown in prostate cells. Recent development in single cell sequencing has made it possible to combine ATAC-seq and RNA-seq to determine genome-wide linkages between chromatin accessibilities and gene expression. To test the feasibility of using single cell multiome sequencing in dissecting regulatory linkages between chromatin accessibilities and gene expressions, we applied 10X Multiome ATAC + Gene Expression platform to simultaneously encapsulate Tn5 transposase tagged nuclei from multiple prostate cell lines. Based on these multiomic data, we developed subsampling linkage analysis to identify linkage associations between open chromatin and gene expressions. Moreover, we implemented an innovative analytical method to investigate RNA expression alterations related to germline variant locus accessibilities at single cell levels, i.e., expression quantitate accessible loci (eQAL) analysis. Our data and methodology will complement traditional eQTL analysis and foresee more genetic applications aiming to clarify regulatory elements by single cell sequencing.

overall_design: Multiomic profilings in human prostate cell lines were captured using 10x Multiome ATAC + Gene Expression assay, and targeted hybridization enrichment was further used to collect signals on eQTL locus.


title: TET2 regulates histone H2AK119ub and leukemogenesis through LTR RNA m5C oxidation [seq_RNA-caRNA]

overall_design: Chromatin-associated RNA-seq in mESC


title: TET2 regulates histone H2AK119ub and leukemogenesis through LTR RNA m5C oxidation [seq_DNA-CUTandTag]

overall_design: CUT&Tag-seq in mESC, mouse LK and K562 cells


title: TET2 regulates histone H2AK119ub and leukemogenesis through LTR RNA m5C oxidation [seq_RNA-caRNA-m5C-MeRIP]

type: Methylation profiling by high throughput sequencing

overall_design: caRNA m5C MeRIP-seq in mESC and K562 cells


title: Insights into Brominated Flame Retardant Neurotoxicity: Mechanisms of Hippocampal Neural Cell Death and Brain Region-Specific Transcriptomic Shifts in Mice

status: Public on Jul 28 2024

city: Detroit

first: Brian

last: Cummings

address: 259 Mack Avenue

department: College of Pharmacy and Health Sciences

institute: Wayne State University

summary: Brominated Flame Retardants (BFRs) reduce flammability in a wide range of products including electronics, carpets, and paint, but leach into the environment to result in continuous, population-level exposure. Epidemiology studies have correlated BFR exposure with neurological problems, including alterations in learning and memory. This study investigated the molecular mechanisms mediating BFR-induced cell death in hippocampal cells and clarified the impact of HBCD exposure on gene transcription in the hippocampus, dorsal striatum, and frontal cortex of male mice. Hippocampal derived HT-22 cell exposure to tetrabromobisphenol-A (TBBPA), hexabromocyclododecane (HBCD), or 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) (current, phasing out, and phased out BFRs, respectively) induced time, concentration, and chemical-dependent cellular and nuclear morphological alterations indicative of apoptosis, which aligned with alterations in cell cycle and increases in annexin V staining. All three BFRs increased p53 and p21 expression; however, inhibition of p53 nuclear translocation using pifthrin-a did not decrease cell death. Transcriptomic analysis upon low (10 nM) and cytotoxic (10 μM) BFR exposure indicated that HBCD and BDE-47 altered genes mediating autophagy-related pathways. Further evaluation showed BFR exposure increased LC3-II conversion and autophagosome formation, and co-exposure with the autophagy inhibitor 3-methyladenine (3-MA) attenuated cytotoxicity. Transcriptomic assessment of select brain regions from subchronically HBCD-exposed male mice demonstrated alteration of genes mediating vesicular transport, with greater impact on the frontal cortex and dorsal striatum compared to the dorsal and ventral hippocampus. These data demonstrate that BFRs can induce chemical-dependent autophagy in neural cells in vitro and provide evidence that BFRs induce region-specific transcriptomic effects in the brain.

overall_design: To investigate the impact of brominated flame retardants on the brain and neural cell populations, HT-22 cells were treated with 10 nM or 10 µM TBBPA, HBCD, or BDE-47 for 48 hr. Results were compared to cells treated with a DMSO vehicle control. Alternatively, 8 wk old male mice were given peanut butter pellets containing 1 mg/kg HBCD once every 3 days for 28 days (10 doses). Following completion of the dosing period, frontal cortex, dorsal striatum, dorsal hippocampus, ventral hippocampus, liver, and kidney tissues were collected for RNA-Sequencing. Results were compared to peanut butter only vehicle control.

first: Naomi

last: Kramer


title: Next Generation Sequencing (NGS) for the identification of markers disregulated in B-ALL cells following activation with the agonist CD40 antibody.

city: Dijon

first: Romain

last: Boidot

address: 1, rue Pr Marion

country: France

institute: CGFL

summary: The goal of this study was to identify through NGS transcriptomic (RNAseq), transcripts up and down-regulated, following the i.v. treatment of B-ALL Patient-Derived Xenotransplanted (PDX) mice (two models; #1 and #2) with anti-CD40 agonist antibody.

overall_design: Total mRNA were extracted from hCD45+ B-ALL cells purified from the BM of PDX-mice.

first: Ronan

last: Quéré

first: Corentin

last: Richard


title: TET2 regulates histone H2AK119ub and leukemogenesis through LTR RNA m5C oxidation [seq_DNA-ATAC]

overall_design: ATAC-seq in mESC and mouse LK cells


title: Exosomal miR-194 from adipose-derived stem cells impedes hypertrophic scar formation through targeting TGF-β1

status: Public on Jul 24 2024

city: Harbin

first: Lijun

last: Hao

address: 23 Youzheng Street

institute: the First Affiliated Hospital of Harbin Medical University

summary: Hypertrophic scars, which result from aberrant fibrosis and disorganized collagen synthesis by skin fibroblasts, emerge due to disrupted wound healing processes. These scars present significant psychosocial and functional challenges to affected individuals. The current treatment limitations largely arise from an incomplete understanding of the underlying mechanisms of hypertrophic scar development. Recent studies, however, have shed light on the potential of exosomal non-coding RNAs interventions to mitigate hypertrophic scar proliferation. This research assesses the impact of exosomes derived from adipose-derived stem cells (ADSCs-Exos) on hypertrophic scar formation using a rabbit ear model. We employed Hematoxylin and Eosin staining, Masson’s Trichrome staining, and Immunohistochemical staining techniques to track scar progression. Our comprehensive analysis encompassed the differential expression of non-coding RNAs, enrichment analyses of functional pathways, protein-protein interaction studies, and miRNA-mRNA interaction investigations. The results reveal a marked alteration in the expression levels of long non-coding RNAs and microRNAs following ADSCs-Exos treatment, with little changes observed in circular RNAs. Notably, miR-194 emerges as a critical regulator within the signaling pathways that govern hypertrophic scar formation. Dual-luciferase assays indicated a significant reduction in the promoter activity of TGF-β1 after miR-194 overexpression. Quantitative reverse transcription PCR and Western blotting assays further validated the decrease in TGF-β1 expression in the treated samples. Moreover, the treatment resulted in diminished levels of inflammatory markers IL-1β, TNF-α, and IL-10. In vivo evidence strongly supports the role of miR-194 in attenuating hypertrophic scar formation through the suppression of TGF-β1. Our findings endorse the strategic use of ADSCs-Exos, particularly through miR-194 modulation, as an effective strategy for reducing scar formation and lowering pro-inflammatory and fibrotic indicators like TGF-β1. Therefore, this study advocates for the targeted application of ADSCs-Exos, with an emphasis on miR-194 modulation, as a promising approach to managing proliferative scarring.

overall_design: Six female New Zealand White rabbits underwent a one-week acclimatization period. After aseptic preparation, six full-thickness wounds were created on the ventral surface of each ear. Each rabbit was housed individually and given antibiotics and analgesics post-surgery. The rabbits were randomly assigned to either a control group or an ADSCs-Exos treatment group (three rabbits per group). Wound care included the application of saline or ADSCs-Exos (100 µg/2 ml) for the first three days post-injury. Scar progression was monitored, and tissue samples were collected for histological analysis on days 3, 7, 14, and 21. Scar tissues from both the control group and the ADSCs-Exos treated group were collected on post-treatment day 21 for total RNA extraction, followed by RNA-seq library construction. RNA sequencing libraries were constructed from the extracted scar tissues. RNAs were selected, ligated to adaptors, reverse-transcribed to cDNA, and amplified. Specific fragments were isolated using PAGE gel electrophoresis, and quality was assessed using Kapa qPCR and Agilent TapeStation. Libraries meeting quality standards were sequenced on an Illumina NovaSeq 6000. The expression profiling of lncRNAs, mRNAs, and circRNAs was subsequently conducted using the sequencing data.

first: Zhishan

last: Xu

first: Yuan

last: Tian


title: A novel adjuvant formulation induces robust Th1/Th17 memory and mucosal recall responses in Non-Human Primates

city: Copenhagen

first: Tu

last: Hu

address: 5 Artillerivej

department: Infectious Disease Immunology

country: Denmark

institute: Statens Serum Institut

summary: After clean drinking water, vaccination is the most impactful global health intervention. However, development of new vaccines against difficult-to-target diseases is hampered by the lack of diverse adjuvants for human use. Of particular interest, none of the currently available adjuvants induce Th17 cells. Here, we develop and test an improved liposomal adjuvant, termed CAF®10b, that incorporates a TLR-9 agonist. In a head-to-head study in non-human primates (NHPs), immunization with antigen adjuvanted with CAF®10b induced significantly increased antibody and cellular immune responses compared to previous CAF® adjuvants, already in clinical trials. This was not seen in the mouse model, demonstrating that adjuvant effects can be highly species specific. Importantly, intramuscular immunization of NHPs with CAF®10b induced robust Th17 responses that were observed in circulation half a year after vaccination. Furthermore, subsequent instillation of unadjuvanted antigen into the skin and lungs of these memory animals led to significant recall responses including transient local lung inflammation observed by Positron Emission Tomography-Computed Tomography (PET-CT), elevated antibody titers, and expanded systemic and local Th1 and Th17 responses, including >20% antigen-specific T cells in the bronchoalveolar lavage. Overall, CAF®10b demonstrated an adjuvant able to drive true memory antibody, Th1 and Th17 vaccine-responses across rodent and primate species, supporting its translational potential.

overall_design: Ten cynomolgus macaques were enrolled in the study, and randomized into two groups (CAF09hi and CAF10b). The administration of the vaccines followed a two-dose intramuscular immunization schedule, with a spacing of four weeks between the doses. Blood samples were collected at three timepoints: (1) at the baseline, (2) on day 1 after the first immunization, and (3) on day 1 after the second immunization.

first: Joshua

last: Woodworth

first: Vanessa

last: Contreras

first: Dennis

last: Christensen

first: Thibaut

last: Naninck

first: Nidhal

last: Kahlaoui

first: Anne-Sophie

last: Gallouët

first: Sébastien

last: Langlois

first: Emma

last: Burban

first: Candie

last: Joly

first: Wesley

last: Gros

first: Nathalie

last: Dereuddre-Bosquet

first: Julie

last: Morin

first: Ming

last: Olsen

first: Ida

last: Rosenkrands

first: Ann-Kathrin

last: Stein

first: Grith

last: Wood

first: Frank

last: Follmann

first: Thomas

last: Lindenstrøm

first: Roger

last: LeGrand

first: Gabriel

last: Pedersen

first: Rasmus

last: Mortensen


title: TET2 regulates histone H2AK119ub and leukemogenesis through LTR RNA m5C oxidation [seq_RNA-nascentRNA]

first: Xiaoyang

last: Dou

overall_design: RNA synthesis rate was measured with a procedure modified from the protocol Click-iT™ Nascent RNA Capture Kit, for gene expression analysis (Invitrogen, C10365).

first: Zhongyu

last: Zou

first: Chuan

last: He


title: PPIA-mediated stabilization of GAU1-SENP5 triplex activates the oncogene SENP5 drives tumorigenesis

first: He

last: Zhang

state: Shanghai

address: Tongji University, 1239 Siping Road, Yangpu District, Shanghai

institute: School of Life Science and Technology, Tongji University

summary: All DNA interacting with GAU1 lncRNA were detected by triplex

overall_design: The DNA  interacting with GAU1 were pulled down by  triplex assay.

first: Xiaoyu


title: Exosomal miR-194 from adipose-derived stem cells impedes hypertrophic scar formation through targeting TGF-β1 [miRNA]

first: Lijun

last: Hao

overall_design: Six female New Zealand White rabbits underwent a one-week acclimatization. After aseptic preparation, six full-thickness wounds were created on the ventral surface of each ear. Each rabbit was housed individually and given antibiotics and analgesics post-surgery. The rabbits were randomly assigned to either a control group or the ADSCs-Exos treatment group (three rabbits per group). Wound care included the application of saline or ADSCs-Exos (100 µg/2 ml) for the first three days post-injury. Scar progression was monitored, and tissue samples were collected for histological analysis on days 3, 7, 14, and 21. Scar tissues from both the control group and the ADSCs-Exos treated group were collected on post-treatment day 21 to extract total RNA, followed by RNA-seq library construction. Small RNA sequencing libraries were then constructed from the extracted scar tissues. Small RNAs were selected, ligated to adaptors, reverse-transcribed to cDNA, and amplified. Specific fragments were isolated using PAGE gel electrophoresis, and quality was assessed with Kapa qPCR and Agilent TapeStation. Libraries meeting quality standards were sequenced on an Illumina NovaSeq 6000. miRNA expression profiling was subsequently conducted using the sequencing data.

first: Zhishan

last: Xu

first: Yuan

last: Tian


title: Vascular and perivascular cell profiling reveals the molecular and cellular bases of blood-brain barrier heterogeneity

status: Public on Jul 23 2024

city: Boston

first: Sarah

last: Pfau

state: MA

address: 220 Longwood Avenue

institute: Harvard Medical School

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

overall_design: Refer to individual Series


title: Systematic surveillance of SARS-CoV-2 reveals dynamics of variant mutagenesis and transmission in a large urban population II

city: Toronto

first: Jeff

last: Wrana

state: Ontario

address: 600 University Avenue

country: Canada

institute: Lunenfeld-Tanenbaum Research Institute

summary: Highly mutable pathogens generate viral diversity that impacts virulence, transmissibility, treatment, and thwarts acquired immunity.  We previously described C19-SPAR-Seq, a high-throughput, next-generation sequencing platform to detect SARS-CoV-2 that we deployed to systematically profile variant dynamics of SARS-CoV-2 for over 3 years in a large, North American urban environment (Toronto, Canada). Sequencing of the ACE2 receptor binding motif and polybasic furin cleavage site of Spike in over 70,000 patients revealed that population sweeps of canonical variants of concern (VOCs) occurred in repeating wavelets. Furthermore, we found that subvariants and putative quasi-species with alterations characteristic of future VOCs and/or predicted to be functionally important arose frequently, but always extinguished. Systematic screening of functionally relevant domains in pathogens could thus provide a powerful tool for monitoring spread and mutational trajectories, particularly those with zoonotic potential.

sample_organism: Severe acute respiratory syndrome coronavirus 2

overall_design: RNAseq and barcode analysis for 1987 human nasopharyngeal swabs for SARS-CoV-2, with 24 negative swabs and 43 synthetic controls.

first: Marie-Ming

last: Aynaud

first: Lauren

last: Caldwell

first: Khalid

middle: N

last: Al-Zahrani

first: Seda

last: Barutcu

first: Kin

last: Chan

first: Andreea

last: Obersterescu

first: Abiodun

last: Ogunjimi

first: Min

last: Jin

first: Kathleen-Rose

last: Zakoor

first: Shyam

last: Patel

first: Ron

last: Padilla

first: Mark

last: Jen

first: Princess Mae

last: Veniegas

first: Nursrin

last: Dewsi

first: Filiam

last: Yonathan

first: Lucy

first: Amelia

last: Ayson-Fortunato

first: Analiza

last: Aquino

first: Paul

last: Krzyzanowksi

first: Jared

last: Simpson

first: John

last: Bartlett

first: Ilinca

last: Lungu

first: Bradley

last: Wouters

first: James

last: Rini

first: Michael

last: Gekas

first: Susan

last: Poutanen

first: Laurence

last: Pelletier

first: Tony

last: Mazzulli

first: Jeffrey


title: Gain of bipolar disorder-related lncRNA AP1AR-DT in mice induces depressive and anxiety-like behaviors by reducing Negr1-mediated excitatory synaptic transmission [Mouse RNA-seq]

status: Public on Jul 22 2024

city: Guangzhou

first: Cunyou

last: Zhao

state: Guangdong

address: No. 1023-1063, South Sha-tai Road, Baiyun District

institute: Southern Medical University

summary: Bipolar disorder is a complex polygenetic disorder that is characterized by recurrent episodes of depression and mania, the heterogeneity of which is likely complicated by epigenetic modifications that remain to be elucidated. Here, we performed transcriptomic analysis of peripheral blood RNA from monozygotic twins discordant for bipolar disorder and identified a bipolar disorder-associated upregulated long non-coding RNA (lncRNA), AP1AR-DT. We observed that overexpression of AP1AR-DT in the mouse medial prefrontal cortex (mPFC) resulted in a reduction of both the total spine density and the spontaneous excitatory postsynaptic current (sEPSC) frequency of mPFC neurons, as well as depressive and anxiety-like behaviors. A combination of the results of brain transcriptome analysis of AP1AR-DT overexpressing mice brains with the known genes associated with bipolar disorder revealed that NEGR1, which encodes neuronal growth regulator 1, is one of the AP1AR-DT targets and is reduced in vivo upon gain of AP1AR-DT in mice. The results of the present study demonstrated that overexpression of recombinant Negr1 in the mPFC neurons of AP1AR-DTOE mice ameliorates depressive and anxiety-like behaviors and normalizes the reduced excitatory synaptic transmission induced by the gain of AP1AR-DT. Furthermore, the study provides evidence that AP1AR-DT reduces NEGR1 expression by competing for the transcriptional activator NRF1 in the overlapping binding site of the NEGR1 promoter region. The epigenetic and pathophysiological mechanism linking AP1AR-DT to the modulation of excitatory synaptic function provides etiological implications for bipolar disorder.

overall_design: To investigate the function of the DE-lncRNA AP1AR-DT in bipolar disorder, AC109347.1 was overexpressed in mouse.

first: Shufen

last: Li

first: Hongyu

last: Ni

first: Yaping

last: Wang

first: Xiaohui

last: Wu

first: Jianqiang

last: Bi

first: Haiyan

last: Ou

first: Zhongwei

first: Junjiao

last: Ping

first: Zhongju

first: Renhao

last: Chen

first: Qiong

last: Yang

first: Meijun

last: Jiang

first: Liping

last: Cao

first: Tingyun

first: Siqiang

last: Ren


title: Vascular and perivascular cell profiling reveals the molecular and cellular bases of blood-brain barrier heterogeneity [GEOMx]

first: Sarah

last: Pfau

summary: Nanostring GeoMX Whole Transcriptome Analysis performed on pericyte- and perivascular fibroblast-enriched areas of interest in the cortex and median eminence of the mouse brain

overall_design: 53 samples, 16 from the cortex and 37 from the ME from 4 replicate animals

first: S

first: C

last: Gu


title: Gain of bipolar disorder-related lncRNA AP1AR-DT in mice induces depressive and anxiety-like behaviors by reducing Negr1-mediated excitatory synaptic transmission [SK-N-SH RNA-seq]

first: Cunyou

overall_design: To investigate the function of the DE-lncRNA AP1AR-DT in bipolar disorder, AC109347.1 was overexpressed in the SK-N-SH cells.

first: Shufen

first: Hongyu


title: Vascular and perivascular cell profiling reveals the molecular and cellular bases of blood-brain barrier heterogeneity [scRNA-Seq]

summary: Single cell (inDrops) RNA sequencing analysis of median eminence and somatosensory cortex in male, wild type mice

overall_design: Samples of the somatosensory cortex and median eminence of 9-week old, C57BL/6 mice profiled by single-cell RNAseq with inDrops


title: Astrocyte transcriptomic changes along the spatiotemporal progression of Alzheimer’s disease

city: Cambridge

first: Sudeshna

last: Das

address: 65 Landsdowne St

department: Neurology

institute: MGH

summary: Astrocytes are crucial to brain homeostasis, yet their changes along the spatiotemporal progression of Alzheimer’s disease (AD) neuropathology remain largely unexplored. Here, we performed single- nucleus RNA-sequencing of 628,943 astrocytes from five brain regions representing the stereotypical progression of AD pathology, across 32 donors spanning the entire normal aging-to-severe AD continuum. We discovered astrocyte gene expression trajectories that are differentially activated or suppressed at various regions and disease stages. We mapped out several unique astrocyte subclusters that exhibited varying responses to neuropathology across the AD-vulnerable neural network (spatial axis) or AD pathology stage (temporal axis). The proportion of homeostatic, intermediate, and reactive astrocytes changed solely along the spatial axis, whereas two other unique subclusters changed along the temporal axis. One of these, a trophic factor-rich subcluster, declined along pathology stage, whereas the other, defined by proteostasis and metabolic genes, increased in late-stage but unexpectedly returned to baseline levels in end-stage, suggesting exhaustion of response with chronic exposure to neuropathology. Our study underscores the complex and dynamic nature of astrocytic responses in AD and our findings are available at https://ad-progression-atlas.partners.org

overall_design: Using an enrichment strategy consisting of depleting NeuN+ve neurons and OLIG2+ve oligodendrocytes via fluorescence-activated nuclei sorting (FANS) we obtained a total of 628,943 astrocyte nuclei from five brain regions of 32 individuals with autopsy findings along the normal aging-to-severe AD neuropathological continuum. The five brain regions were selected to represent the hierarchical spreading of pTau NFTs along brain networks as categorized by the Braak NFT staging system and included entorhinal cortex (EC), inferior temporal gyrus (ITG, Brodmann Area BA20), dorsolateral prefrontal cortex (PFC, BA46), visual association cortex (V2, BA18/19), and primary visual cortex (V1, BA17).

first: Alberto

last: Serrano-Pozo

first: Huan

first: Zhaozhi

first: Clara

last: Muñoz-Castro

first: Methasit

last: Jaisaaad

first: Molly

last: Healey

first: Lindsay

last: Welikovitch

first: Rojashree

last: Jayakumar

first: Annie

last: Bryant

first: Ayush

last: Noori

first: Theresa

last: Connors

first: Miwei

last: Hu

first: Karen

first: Fan

last: Liao

first: Gen

last: Lin

first: Timothy

last: Pastika

first: Joseph

last: Tamm

first: Aicha

last: Abdourahman

first: Taekyung

last: Kwon

first: Rachel

middle: E

last: Bennet

first: Maya

last: Woodbury

first: Astrid

last: Watcher

first: Robert

middle: V

last: Talanian

first: Knut

last: Biber

first: Eric

last: Karran

first: Bradley

middle: T

last: Hyman


title: Epigenetic and oncogenic inhibitors cooperatively drive differentiation and kill KRAS-mutant colorectal cancers [CRC cell lines]

first: Amy

last: Schade

address: 77 Avenue Louis Pasteur

department: Medicine

institute: Brigham and Women's Hospital

summary: Current treatments for KRAS-mutant colorectal cancers (CRCs) are often limited by cellular plasticity and rewiring responses. Here we describe a promising therapeutic strategy that simultaneously targets epigenetic and oncogenic signals. Specifically, we show that inhibitors of the histone methyltransferase, EZH2, synergize with various RAS pathway inhibitors and promote dramatic tumor regression in vivo. Together these agents cooperatively suppress WNT-driven transcription and drive CRCs into a more differentiated cell state by inducing the Groucho/TLE corepressor, TLE4, along with a network of WNT pathway inhibitors and intestinal differentiation proteins. However, these agents also induce the pro-apoptotic protein BMF, which subsequently kills these more differentiated cells. Accordingly, cell death can be prevented by activating β-catenin, blocking differentiation, or by ablating BMF expression. Collectively, these studies reveal a new therapeutic approach for treating KRAS-mutant CRCs and illustrate a critical convergence of EZH2 and RAS on oncogenic WNT signals, intestinal differentiation, and apoptosis.

overall_design: Colorectal cancer cell lines (LOVO, SW620, SK-CO1, and LS513) were treated with vehicle, tazemetostat (EZH2i), and/or trametinib (MEKi) or MRTX1133 (KRASi) for LS513 cells.  Cells were pretreated with DMSO or EZH2i for 5 days, seeded into 6cm plates at 300,000-350,000 cells per plate, and treated with DMSO, MEKi or KRASi, with and without EZH2i the following day. Cells were collected 16-24 hours after combined treatment before onset of cell death. RNA was isolated and sequenced using NGS.

first: Patrick

last: Loi

last: Cichowski


title: Epigenetic and oncogenic inhibitors cooperatively drive differentiation and kill KRAS-mutant colorectal cancers [LOVO sgTLE4]

overall_design: Colorectal cancer cell line, LOVO, were transduced with lentivirus to ectopically express an empty vector or a constitutively active form of B-catenin, and then treated with vehicle, tazemetostat (EZH2i), and/or trametinib (MEKi). Cells were pretreated with DMSO or EZH2i (tazemetostat at 5uM) for 5 days, and then seeded into 6cm plates of 300,000 to 350,000 cells per plate. The following day, cells were treated with DMSO, MEKi (50nM trametinib), with and without EZH2i.  Cells were collected 16-24 hours after combined treatment before onset of cell death.


title: Pre-existing skin-resident CD8 and γδ T cell circuits mediate immune response in Merkel cell carcinoma and Predict immunotherapy efficacy [scRNA_tissue]

city: Chicago

first: Jaehyuk

last: Choi

state: Illinois

address: 303 E. Superior St. 5-220

department: Dermatology

institute: Northwestern University

summary: Merkel Cell Carcinoma (MCC) is an aggressie skin cancer with limiterd treatment and low response rates to Immune Checkpoint Blockade (ICB) therapy. We compiled the largest sc database of MCC tumor samples and matched blood to identify tumor gener modules that Predict ICB response.

overall_design:
MCC tumor and matched blood samples were used for bulk and single-cell RNA-seq.

**Raw data was deposited in dbGaP (phs003629)**

first: Zachary

middle: Z

last: Reinstein

first: Yue

last: Zhang

first: Oscar

last: Ospina

first: Matt

last: Nichols

first: Victoria

last: Chu

first: Alvaro

last: de Mingo Pulido

first: Karol

last: Prieto

first: Johnathan

last: Ngyuen

first: Rui

last: Yin

first: Carlos

last: de Moran Segura

first: Ahmed

last: Usman

first: Brittney

last: Sell

first: Spencer

last: Ng

first: Janis

last: de la Iglesia

first: Sunandana

last: Chandra

first: Jeffery

last: Sosman

first: Raymond

middle: J

last: Cho

middle: B

last: Cheng

first: Ellie

last: Ivanova

first: Sergei

last: Koralov

first: Robbert

last: Slebos

first: Christine

last: Chung

first: Nikhill

middle: I

last: Khushalani

first: Jane

last: Messina

first: Amod

last: Sarnaik

middle: S

last: Zager

first: Vernon

last: Sondak

first: Charles

last: Vaske

first: Sungjune

last: Kim

first: Andrew

last: Brohl

first: Xinlei

last: Min

first: Brian

last: Pierce

first: Brooke

last: Fridley

first: Kenneth

middle: Y

last: Tsai


title: Epigenetic and oncogenic inhibitors cooperatively drive differentiation and kill KRAS-mutant colorectal cancers [LOVO_BCat]

first: Amy

last: Schade

first: Patrick

last: Loi

first: Karen

last: Cichowski


title: Systematic surveillance of SARS-CoV-2 reveals dynamics of variant mutagenesis and transmission in a large urban population III

first: Jeff

last: Wrana

platform_organism: Severe acute respiratory syndrome coronavirus 2

overall_design: RNAseq and barcode analysis for 1937 human nasopharyngeal swabs for SARS-CoV-2, with 24 negative swabs and 42 synthetic controls  [repeat of previous BC experiment]

first: Marie-Ming

last: Aynaud

first: Lauren

last: Caldwell

first: Khalid

last: Al-Zahrani

first: Seda

last: Barutcu

first: Kin

last: Chan

first: Andreea

last: Obersterescu

first: Abiodun

last: Ogunjimi

first: Min

last: Jin

first: Kathleen-Rose

last: Zakoor

first: Shyam

last: Patel

first: Ron

last: Padilla

first: Mark

last: Jen

first: Princess Mae

last: Veniegas

first: Nursrin

last: Dewsi

first: Filiam

last: Yonathan

first: Lucy

last: Zhang

first: Amelia

last: Ayson-Fortunato

first: Analiza

last: Aquino

first: Paul

last: Krzyzanowski

first: Jared

last: Simpson

first: John

last: Bartlett

first: Ilinca

last: Lungu

first: Bradley

middle: G

last: Wouters

first: James

middle: M

last: Rini

first: Michael

last: Gekas

first: Susan

last: Poutanen

first: Laurence

last: Pelletier

first: Tony

last: Mazzulli

first: Jeffrey