1
|
Li YR, Ling LB, Chao A, Fugmann SD, Yang SY. Transient chromatin decompaction at the start of D. melanogaster male embryonic germline development. Life Sci Alliance 2024; 7:e202302401. [PMID: 38991729 PMCID: PMC11239976 DOI: 10.26508/lsa.202302401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 06/28/2024] [Accepted: 07/01/2024] [Indexed: 07/13/2024] Open
Abstract
Embryonic germ cells develop rapidly to establish the foundation for future developmental trajectories, and in this process, they make critical lineage choices including the configuration of their unique identity and a decision on sex. Here, we use single-cell genomics patterns for the entire embryonic germline in Drosophila melanogaster along with the somatic gonadal precursors after embryonic gonad coalescence to investigate molecular mechanisms involved in the setting up and regulation of the germline program. Profiling of the early germline chromatin landscape revealed sex- and stage-specific features. In the male germline immediately after zygotic activation, the chromatin structure underwent a brief remodeling phase during which nucleosome density was lower and deconcentrated from promoter regions. These findings echoed enrichment analysis results of our genomics data in which top candidates were factors with the ability to mediate large-scale chromatin reorganization. Together, they point to the importance of chromatin regulation in the early germline and raise the possibility of a conserved epigenetic reprogramming-like process required for proper initiation of germline development.
Collapse
Affiliation(s)
- Yi-Ru Li
- https://ror.org/00d80zx46 Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Li Bin Ling
- https://ror.org/00d80zx46 Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Angel Chao
- https://ror.org/02dnn6q67 Department of Obstetrics and Gynecology, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Sebastian D Fugmann
- https://ror.org/00d80zx46 Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- https://ror.org/00d80zx46 Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- https://ror.org/02dnn6q67 Department of Nephrology, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Shu Yuan Yang
- https://ror.org/00d80zx46 Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- https://ror.org/00d80zx46 Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- https://ror.org/02dnn6q67 Department of Obstetrics and Gynecology, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| |
Collapse
|
2
|
He J, Gao L, Wang P, Chan WK, Zheng Y, Zhang Y, Sun J, Li X, Wang J, Li XH, Chen H, Yang Z, Wang Y. Prdm1 positively regulates liver Group 1 ILCs cancer immune surveillance and preserves functional heterogeneity. eLife 2024; 13:RP92948. [PMID: 39133873 PMCID: PMC11318973 DOI: 10.7554/elife.92948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024] Open
Abstract
Group 1 innate lymphoid cells (ILCs) comprise conventional natural killer (cNK) cells and type 1 innate lymphoid cells (ILC1s). The main functions of liver cNK cells and ILC1s not only include directly killing target cells but also regulating local immune microenvironment of the liver through the secretion of cytokines. Uncovering the intricate mechanisms by which transcriptional factors regulate and influence the functions of liver cNK cells and ILC1s, particularly within the context of liver tumors, presents a significant opportunity to amplify the effectiveness of immunotherapies against liver malignancies. Using Ncr1-drived conditional knockout mouse model, our study reveals the regulatory role of Prdm1 in shaping the composition and maturation of cNK cells. Although Prdm1 did not affect the killing function of cNK cells in an in vivo cytotoxicity model, a significant increase in cancer metastasis was observed in Prdm1 knockout mice. Interferon-gamma (IFN-γ), granzyme B, and perforin secretion decreased significantly in Prdm1-deficient cNK cells and liver ILC1s. Single-cell RNA sequencing (scRNA-seq) data also provided evidences that Prdm1 maintains functional subsets of cNK cells and liver ILC1s and facilitates communications between cNK cells, liver ILC1s, and macrophages. The present study unveiled a novel regulatory mechanism of Prdm1 in cNK cells and liver ILC1s, showing promising potential for developing innovative immune therapy strategies against liver cancer.
Collapse
Affiliation(s)
- Jitian He
- Institute of Medical Engineering & Translational Medicine, Tianjin UniversityTianjinChina
- Organ Transplant Center, The First Affiliated Hospital of Sun Yat-sen UniversityGuangzhouChina
| | - Le Gao
- Institute of Medical Engineering & Translational Medicine, Tianjin UniversityTianjinChina
| | - Peiying Wang
- Institute of Medical Engineering & Translational Medicine, Tianjin UniversityTianjinChina
| | - Wing Keung Chan
- Department of Internal Medicine, Division of Hematology, The Ohio State UniversityColumbusUnited States
| | - Yiran Zheng
- Institute of Medical Engineering & Translational Medicine, Tianjin UniversityTianjinChina
| | - Yumo Zhang
- Institute of Medical Engineering & Translational Medicine, Tianjin UniversityTianjinChina
| | - Jiaman Sun
- Institute of Medical Engineering & Translational Medicine, Tianjin UniversityTianjinChina
| | - Xue Li
- Department of Basic Medicine, Haihe Hospital, Tianjin UniversityTianjinChina
| | - Jiming Wang
- Tianjin Economic-Technological Development Area (TEDA) HospitalTianjinChina
| | - Xiao-Hong Li
- Institute of Medical Engineering & Translational Medicine, Tianjin UniversityTianjinChina
| | - Huaiyong Chen
- Department of Basic Medicine, Haihe Hospital, Tianjin UniversityTianjinChina
- College of Pulmonary and Critical Care Medicine, 8th Medical Center, Chinese PLA General HospitalBeijingChina
- Tianjin Key Laboratory of Lung Regenerative MedicineTianjinChina
| | - Zhouxin Yang
- Zhejiang Provincial Key Lab of Geriatrics and Geriatrics Institute of Zhejiang Province, Zhejiang HospitalHangzhouChina
| | - Youwei Wang
- Institute of Medical Engineering & Translational Medicine, Tianjin UniversityTianjinChina
| |
Collapse
|
3
|
Rodrigues-Amorim D, Bozzelli PL, Kim T, Liu L, Gibson O, Yang CY, Murdock MH, Galiana-Melendez F, Schatz B, Davison A, Islam MR, Shin Park D, Raju RM, Abdurrob F, Nelson AJ, Min Ren J, Yang V, Stokes MP, Tsai LH. Multisensory gamma stimulation mitigates the effects of demyelination induced by cuprizone in male mice. Nat Commun 2024; 15:6744. [PMID: 39112447 PMCID: PMC11306744 DOI: 10.1038/s41467-024-51003-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 07/08/2024] [Indexed: 08/10/2024] Open
Abstract
Demyelination is a common pathological feature in a wide range of diseases, characterized by the loss of myelin sheath and myelin-supporting oligodendrocytes. These losses lead to impaired axonal function, increased vulnerability of axons to damage, and result in significant brain atrophy and neuro-axonal degeneration. Multiple pathomolecular processes contribute to neuroinflammation, oligodendrocyte cell death, and progressive neuronal dysfunction. In this study, we use the cuprizone mouse model of demyelination to investigate long-term non-invasive gamma entrainment using sensory stimulation as a potential therapeutic intervention for promoting myelination and reducing neuroinflammation in male mice. Here, we show that multisensory gamma stimulation mitigates demyelination, promotes oligodendrogenesis, preserves functional integrity and synaptic plasticity, attenuates oligodendrocyte ferroptosis-induced cell death, and reduces brain inflammation. Thus, the protective effects of multisensory gamma stimulation on myelin and anti-neuroinflammatory properties support its potential as a therapeutic approach for demyelinating disorders.
Collapse
Grants
- R01 AG069232 NIA NIH HHS
- R01 AT011460 NCCIH NIH HHS
- R01 NS122742 NINDS NIH HHS
- R56 AG069232 NIA NIH HHS
- We would like to acknowledge the following individuals and organizations for their support: Fundacion Bancaria la Caixa, The JPB Foundation, Carol and Gene Ludwig Family Foundation, Lester A. Gimpelson, Eduardo Eurnekian, The Dolby Family, Kathy and Miguel Octavio, the Marc Haas Foundation, Ben Lenail and Laurie Yoler, and NIH RO1 grants AG069232, AT011460 and R01NS122742 to L.-H.T.
Collapse
Affiliation(s)
- Daniela Rodrigues-Amorim
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - P Lorenzo Bozzelli
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - TaeHyun Kim
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Liwang Liu
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Cheng-Yi Yang
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mitchell H Murdock
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Fabiola Galiana-Melendez
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Brooke Schatz
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alexis Davison
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Md Rezaul Islam
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Dong Shin Park
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ravikiran M Raju
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Division of Newborn Medicine, Harvard Medical School, Boston Children's Hospital, Boston, MA, USA
| | - Fatema Abdurrob
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Jian Min Ren
- Cell Signaling Technology, 3 Trask Lane, Danvers, MA, USA
| | - Vicky Yang
- Cell Signaling Technology, 3 Trask Lane, Danvers, MA, USA
| | | | - Li-Huei Tsai
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
| |
Collapse
|
4
|
Reiner BC, Chehimi SN, Merkel R, Toikumo S, Berrettini WH, Kranzler HR, Sanchez-Roige S, Kember RL, Schmidt HD, Crist RC. A single-nucleus transcriptomic atlas of medium spiny neurons in the rat nucleus accumbens. Sci Rep 2024; 14:18258. [PMID: 39107568 PMCID: PMC11303397 DOI: 10.1038/s41598-024-69255-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 08/02/2024] [Indexed: 08/10/2024] Open
Abstract
Neural processing of rewarding stimuli involves several distinct regions, including the nucleus accumbens (NAc). The majority of NAc neurons are GABAergic projection neurons known as medium spiny neurons (MSNs). MSNs are broadly defined by dopamine receptor expression, but evidence suggests that a wider array of subtypes exist. To study MSN heterogeneity, we analyzed single-nucleus RNA sequencing data from the largest available rat NAc dataset. Analysis of 48,040 NAc MSN nuclei identified major populations belonging to the striosome and matrix compartments. Integration with mouse and human data indicated consistency across species and disease-relevance scoring using genome-wide association study results revealed potentially differential roles for MSN populations in substance use disorders. Additional high-resolution clustering identified 34 transcriptomically distinct subtypes of MSNs definable by a limited number of marker genes. Together, these data demonstrate the diversity of MSNs in the NAc and provide a basis for more targeted genetic manipulation of specific populations.
Collapse
Affiliation(s)
- Benjamin C Reiner
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Samar N Chehimi
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Riley Merkel
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biobehavioral Health Sciences, School of Nursing, University of Pennsylvania, Philadelphia, PA, USA
| | - Sylvanus Toikumo
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Wade H Berrettini
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Henry R Kranzler
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Mental Illness Research, Education and Clinical Center, Crescenz VAMC, Philadelphia, PA, USA
| | - Sandra Sanchez-Roige
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Institute for Genomic Medicine, University of California San Diego, San Diego, CA, USA
| | - Rachel L Kember
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Mental Illness Research, Education and Clinical Center, Crescenz VAMC, Philadelphia, PA, USA
| | - Heath D Schmidt
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biobehavioral Health Sciences, School of Nursing, University of Pennsylvania, Philadelphia, PA, USA
| | - Richard C Crist
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, 125 South 31st Street, Room 2207, Philadelphia, PA, 19104, USA.
| |
Collapse
|
5
|
Wang L, Wang C, Moriano JA, Chen S, Zuo G, Cebrián-Silla A, Zhang S, Mukhtar T, Wang S, Song M, de Oliveira LG, Bi Q, Augustin JJ, Ge X, Paredes MF, Huang EJ, Alvarez-Buylla A, Duan X, Li J, Kriegstein AR. Molecular and cellular dynamics of the developing human neocortex at single-cell resolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.16.575956. [PMID: 39131371 PMCID: PMC11312442 DOI: 10.1101/2024.01.16.575956] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
The development of the human neocortex is a highly dynamic process and involves complex cellular trajectories controlled by cell-type-specific gene regulation 1 . Here, we collected paired single-nucleus chromatin accessibility and transcriptome data from 38 human neocortical samples encompassing both the prefrontal cortex and primary visual cortex. These samples span five main developmental stages, ranging from the first trimester to adolescence. In parallel, we performed spatial transcriptomic analysis on a subset of the samples to illustrate spatial organization and intercellular communication. This atlas enables us to catalog cell type-, age-, and area-specific gene regulatory networks underlying neural differentiation. Moreover, combining single-cell profiling, progenitor purification, and lineage-tracing experiments, we have untangled the complex lineage relationships among progenitor subtypes during the transition from neurogenesis to gliogenesis in the human neocortex. We identified a tripotential intermediate progenitor subtype, termed Tri-IPC, responsible for the local production of GABAergic neurons, oligodendrocyte precursor cells, and astrocytes. Remarkably, most glioblastoma cells resemble Tri-IPCs at the transcriptomic level, suggesting that cancer cells hijack developmental processes to enhance growth and heterogeneity. Furthermore, by integrating our atlas data with large-scale GWAS data, we created a disease-risk map highlighting enriched ASD risk in second-trimester intratelencephalic projection neurons. Our study sheds light on the gene regulatory landscape and cellular dynamics of the developing human neocortex.
Collapse
|
6
|
Moerkens R, Mooiweer J, Ramírez-Sánchez AD, Oelen R, Franke L, Wijmenga C, Barrett RJ, Jonkers IH, Withoff S. An iPSC-derived small intestine-on-chip with self-organizing epithelial, mesenchymal, and neural cells. Cell Rep 2024; 43:114247. [PMID: 38907996 DOI: 10.1016/j.celrep.2024.114247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/10/2024] [Accepted: 05/02/2024] [Indexed: 06/24/2024] Open
Abstract
Human induced pluripotent stem cell (hiPSC)-derived intestinal organoids are valuable tools for researching developmental biology and personalized therapies, but their closed topology and relative immature state limit applications. Here, we use organ-on-chip technology to develop a hiPSC-derived intestinal barrier with apical and basolateral access in a more physiological in vitro microenvironment. To replicate growth factor gradients along the crypt-villus axis, we locally expose the cells to expansion and differentiation media. In these conditions, intestinal epithelial cells self-organize into villus-like folds with physiological barrier integrity, and myofibroblasts and neurons emerge and form a subepithelial tissue in the bottom channel. The growth factor gradients efficiently balance dividing and mature cell types and induce an intestinal epithelial composition, including absorptive and secretory lineages, resembling the composition of the human small intestine. This well-characterized hiPSC-derived intestine-on-chip system can facilitate personalized studies on physiological processes and therapy development in the human small intestine.
Collapse
Affiliation(s)
- Renée Moerkens
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Joram Mooiweer
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Aarón D Ramírez-Sánchez
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Roy Oelen
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands; Oncode Institute, 3521 AL Utrecht, the Netherlands
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands; Oncode Institute, 3521 AL Utrecht, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Robert J Barrett
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; F. Widjaja Foundation Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Iris H Jonkers
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Sebo Withoff
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands.
| |
Collapse
|
7
|
Yalcinbas EA, Ajanaku B, Nelson ED, Garcia-Flores R, Eagles NJ, Montgomery KD, Stolz JM, Wu J, Divecha HR, Chandra A, Bharadwaj RA, Bach S, Rajpurohit A, Tao R, Pertea G, Shin JH, Kleinman JE, Hyde TM, Weinberger DR, Huuki-Myers LA, Collado-Torres L, Maynard KR. Transcriptomic analysis of the human habenula in schizophrenia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.26.582081. [PMID: 38463979 PMCID: PMC10925152 DOI: 10.1101/2024.02.26.582081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Pathophysiology of many neuropsychiatric disorders, including schizophrenia (SCZD), is linked to habenula (Hb) function. While pharmacotherapies and deep brain stimulation targeting the Hb are emerging as promising therapeutic treatments, little is known about the cell type-specific transcriptomic organization of the human Hb or how it is altered in SCZD. Here we define the molecular neuroanatomy of the human Hb and identify transcriptomic changes in individuals with SCZD compared to neurotypical controls. Utilizing Hb-enriched postmortem human brain tissue, we performed single nucleus RNA-sequencing (snRNA-seq; n=7 neurotypical donors) and identified 17 molecularly defined Hb cell types across 16,437 nuclei, including 3 medial and 7 lateral Hb populations, several of which were conserved between rodents and humans. Single molecule fluorescent in situ hybridization (smFISH; n=3 neurotypical donors) validated snRNA-seq Hb cell types and mapped their spatial locations. Bulk RNA-sequencing and cell type deconvolution in Hb-enriched tissue from 35 individuals with SCZD and 33 neurotypical controls yielded 45 SCZD-associated differentially expressed genes (DEGs, FDR < 0.05), with 32 (71%) unique to Hb-enriched tissue. eQTL analysis identified 717 independent SNP-gene pairs (FDR < 0.05), where either the SNP is a SCZD risk variant (16 pairs) or the gene is a SCZD DEG (7 pairs). eQTL and SCZD risk colocalization analysis identified 16 colocalized genes. These results identify topographically organized cell types with distinct molecular signatures in the human Hb and demonstrate unique genetic changes associated with SCZD, thereby providing novel molecular insights into the role of Hb in neuropsychiatric disorders. One Sentence Summary Transcriptomic analysis of the human habenula and identification of molecular changes associated with schizophrenia risk and illness state.
Collapse
|
8
|
Gunter-Rahman F, Mallett S, White F, Jacques PÉ, Raju RM, Hivert MF, Lee EA. Maternal obesity and offspring neurodevelopment are associated with hypoxic gene expression in term human placenta. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.10.602900. [PMID: 39026777 PMCID: PMC11257614 DOI: 10.1101/2024.07.10.602900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
One third of women in the United States are affected by obesity during pregnancy. Maternal obesity (MO) is associated with an increased risk of neurodevelopmental and metabolic disorders in the offspring. The placenta, located at the maternal-fetal interface, is a key organ determining fetal development and likely contributes to programming of long-term offspring health. We profiled the term placental transcriptome in humans (pre-pregnancy BMI 35+ [MO condition] or 18.5-25 [lean condition]) using single-nucleus RNA-seq to compare expression profiles in MO versus lean conditions, and to reveal potential mechanisms underlying offspring disease risk. We recovered 62,864 nuclei of high quality from 10 samples each from the maternal-facing and fetal-facing sides of the placenta. On both sides in several cell types, MO was associated with upregulation of hypoxia response genes. On the maternal-facing side only, hypoxia gene expression was associated with offspring neurodevelopmental measures, in Gen3G, an independent pregnancy cohort with bulk placental tissue RNA-seq. We leveraged Gen3G to determine genes that correlated with impaired neurodevelopment and found these genes to be most highly expressed in extravillous trophoblasts (EVTs). EVTs further showed the strongest correlation between neurodevelopment impairment gene scores (NDIGSs) and the hypoxia gene score. We reanalyzed gene expression of cultured EVTs, and found increased NDIGSs associated with exposure to hypoxia. Among EVTs, accounting for the hypoxia gene score attenuated 44% of the association between BMI and NDIGSs. These data suggest that hypoxia in EVTs may be a key process in the neurodevelopmental programming of fetal exposure to MO.
Collapse
|
9
|
Jin M, Ma Z, Zhang H, Papetti AV, Dang R, Stillitano AC, Goldman SA, Jiang P. Co-Transplantation-Based Human-Mouse Chimeric Brain Models to Study Human Glial-Glial and Glial-Neuronal Interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.03.601990. [PMID: 39005270 PMCID: PMC11244967 DOI: 10.1101/2024.07.03.601990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Human-mouse chimeric brain models, generated by transplanting human induced pluripotent stem cell (hiPSC)-derived neural cells, are valuable for studying the development and function of human neural cells in vivo. Understanding glial-glial and glial-neuronal interactions is essential for unraveling the complexities of brain function and developing treatments for neurological disorders. To explore these interactions between human neural cells within an intact brain environment, we employe a co-transplantation strategy involving the engraftment of hiPSC-derived neural progenitor cells along with primitive macrophage progenitors into the neonatal mouse brain. This approach creates human-mouse chimeric brains containing human microglia, macroglia (astroglia and oligodendroglia), and neurons. Using super-resolution imaging and 3D reconstruction techniques, we examine the dynamics between human neurons and glia, unveiling human microglia engulfing immature human neurons, microglia pruning synapses of human neurons, and significant interactions between human oligodendrocytes and neurons. Single-cell RNA sequencing analysis of the chimeric brain uncovers a close recapitulation of the human glial progenitor cell population, along with a dynamic stage in astroglial development that mirrors the processes found in the human brain. Furthermore, cell-cell communication analysis highlights significant neuronal-glial and glial-glial interactions, especially the interaction between adhesion molecules neurexins and neuroligins. This innovative co-transplantation model opens up new avenues for exploring the complex pathophysiological mechanisms underlying human neurological diseases. It holds particular promise for studying disorders where glial-neuronal interactions and non-cell-autonomous effects play crucial roles.
Collapse
Affiliation(s)
- Mengmeng Jin
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
- These authors contributed equally
| | - Ziyuan Ma
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
- These authors contributed equally
| | - Haiwei Zhang
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
- These authors contributed equally
| | - Ava V. Papetti
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
| | - Rui Dang
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
| | | | - Steven A. Goldman
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY, USA
- Center for Translational Neuromedicine, University of Copenhagen Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - Peng Jiang
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
- Lead Contact
| |
Collapse
|
10
|
Oguchi A, Suzuki A, Komatsu S, Yoshitomi H, Bhagat S, Son R, Bonnal RJP, Kojima S, Koido M, Takeuchi K, Myouzen K, Inoue G, Hirai T, Sano H, Takegami Y, Kanemaru A, Yamaguchi I, Ishikawa Y, Tanaka N, Hirabayashi S, Konishi R, Sekito S, Inoue T, Kere J, Takeda S, Takaori-Kondo A, Endo I, Kawaoka S, Kawaji H, Ishigaki K, Ueno H, Hayashizaki Y, Pagani M, Carninci P, Yanagita M, Parrish N, Terao C, Yamamoto K, Murakawa Y. An atlas of transcribed enhancers across helper T cell diversity for decoding human diseases. Science 2024; 385:eadd8394. [PMID: 38963856 DOI: 10.1126/science.add8394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 05/01/2024] [Indexed: 07/06/2024]
Abstract
Transcribed enhancer maps can reveal nuclear interactions underpinning each cell type and connect specific cell types to diseases. Using a 5' single-cell RNA sequencing approach, we defined transcription start sites of enhancer RNAs and other classes of coding and noncoding RNAs in human CD4+ T cells, revealing cellular heterogeneity and differentiation trajectories. Integration of these datasets with single-cell chromatin profiles showed that active enhancers with bidirectional RNA transcription are highly cell type-specific and that disease heritability is strongly enriched in these enhancers. The resulting cell type-resolved multimodal atlas of bidirectionally transcribed enhancers, which we linked with promoters using fine-scale chromatin contact maps, enabled us to systematically interpret genetic variants associated with a range of immune-mediated diseases.
Collapse
Affiliation(s)
- Akiko Oguchi
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akari Suzuki
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Shuichiro Komatsu
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- IFOM ETS - the AIRC Institute of Molecular Oncology, Milan, Italy
| | - Hiroyuki Yoshitomi
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- Department of Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shruti Bhagat
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
| | - Raku Son
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | | | - Shohei Kojima
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Masaru Koido
- Division of Molecular Pathology, Department of Cancer Biology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kazuhiro Takeuchi
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- Department of Medical Systems Genomics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Keiko Myouzen
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Gyo Inoue
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Tomoya Hirai
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Hiromi Sano
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | | | | | - Yuki Ishikawa
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Nao Tanaka
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Shigeki Hirabayashi
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Division of Precision Medicine, Kyushu University Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Riyo Konishi
- Inter-Organ Communication Research Team, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Sho Sekito
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- Department of Nephro-Urologic Surgery and Andrology, Mie University Graduate School of Medicine, Mie University, Tsu, Japan
| | - Takahiro Inoue
- Department of Nephro-Urologic Surgery and Andrology, Mie University Graduate School of Medicine, Mie University, Tsu, Japan
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
- Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
- Folkhalsan Research Center, Helsinki, Finland
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Itaru Endo
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Shinpei Kawaoka
- Inter-Organ Communication Research Team, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Department of Integrative Bioanalytics, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Hideya Kawaji
- Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
- Preventive Medicine and Applied Genomics Unit, RIKEN Center for Integrative Medical Science, Yokohama, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Japan
| | - Kazuyoshi Ishigaki
- Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Hideki Ueno
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- Department of Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshihide Hayashizaki
- K.K. DNAFORM, Yokohama, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Japan
| | - Massimiliano Pagani
- IFOM ETS - the AIRC Institute of Molecular Oncology, Milan, Italy
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi, Milan, Italy
| | - Piero Carninci
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Human Technopole, Milan, Italy
| | - Motoko Yanagita
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Nicholas Parrish
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
- Department of Applied Genetics, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yasuhiro Murakawa
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- IFOM ETS - the AIRC Institute of Molecular Oncology, Milan, Italy
- Department of Medical Systems Genomics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| |
Collapse
|
11
|
Qadir MMF, Elgamal RM, Song K, Kudtarkar P, Sakamuri SS, Katakam PV, El-Dahr SS, Kolls JK, Gaulton KJ, Mauvais-Jarvis F. Single cell regulatory architecture of human pancreatic islets suggests sex differences in β cell function and the pathogenesis of type 2 diabetes. RESEARCH SQUARE 2024:rs.3.rs-4607352. [PMID: 39011095 PMCID: PMC11247939 DOI: 10.21203/rs.3.rs-4607352/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Type 2 and type 1 diabetes (T2D, T1D) exhibit sex differences in insulin secretion, the mechanisms of which are unknown. We examined sex differences in human pancreatic islets from 52 donors with and without T2D combining single cell RNA-seq (scRNA-seq), single nucleus assay for transposase-accessible chromatin sequencing (snATAC-seq), hormone secretion, and bioenergetics. In nondiabetic (ND) donors, sex differences in islet cells gene accessibility and expression predominantly involved sex chromosomes. Islets from T2D donors exhibited similar sex differences in sex chromosomes differentially expressed genes (DEGs), but also exhibited sex differences in autosomal genes. Comparing β cells from T2D vs. ND donors, gene enrichment of female β cells showed suppression in mitochondrial respiration, while male β cells exhibited suppressed insulin secretion. Thus, although sex differences in gene accessibility and expression of ND β cells predominantly affect sex chromosomes, the transition to T2D reveals sex differences in autosomes highlighting mitochondrial failure in females.
Collapse
Affiliation(s)
- Mirza Muhammad Fahd Qadir
- Section of Endocrinology and Metabolism, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
- Southeast Louisiana Veterans Health Care System, New Orleans, LA, USA
- Tulane Center of Excellence in Sex-Based Biology & Medicine, New Orleans, LA, USA
| | - Ruth M. Elgamal
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Keijing Song
- Center for Translational Research in Infection and Inflammation, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Parul Kudtarkar
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Siva S.V.P Sakamuri
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Prasad V. Katakam
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Samir S. El-Dahr
- Department of Pediatrics, Tulane University, School of Medicine, New Orleans, LA, USA
| | - Jay K. Kolls
- Center for Translational Research in Infection and Inflammation, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Kyle J. Gaulton
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Franck Mauvais-Jarvis
- Section of Endocrinology and Metabolism, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
- Southeast Louisiana Veterans Health Care System, New Orleans, LA, USA
- Tulane Center of Excellence in Sex-Based Biology & Medicine, New Orleans, LA, USA
| |
Collapse
|
12
|
Derisoud E, Jiang H, Zhao A, Chavatte-Palmer P, Deng Q. Revealing the molecular landscape of human placenta: a systematic review and meta-analysis of single-cell RNA sequencing studies. Hum Reprod Update 2024; 30:410-441. [PMID: 38478759 PMCID: PMC11215163 DOI: 10.1093/humupd/dmae006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 02/12/2024] [Indexed: 07/02/2024] Open
Abstract
BACKGROUND With increasing significance of developmental programming effects associated with placental dysfunction, more investigations are devoted to improving the characterization and understanding of placental signatures in health and disease. The placenta is a transitory but dynamic organ adapting to the shifting demands of fetal development and available resources of the maternal supply throughout pregnancy. Trophoblasts (cytotrophoblasts, syncytiotrophoblasts, and extravillous trophoblasts) are placental-specific cell types responsible for the main placental exchanges and adaptations. Transcriptomic studies with single-cell resolution have led to advances in understanding the placenta's role in health and disease. These studies, however, often show discrepancies in characterization of the different placental cell types. OBJECTIVE AND RATIONALE We aim to review the knowledge regarding placental structure and function gained from the use of single-cell RNA sequencing (scRNAseq), followed by comparing cell-type-specific genes, highlighting their similarities and differences. Moreover, we intend to identify consensus marker genes for the various trophoblast cell types across studies. Finally, we will discuss the contributions and potential applications of scRNAseq in studying pregnancy-related diseases. SEARCH METHODS We conducted a comprehensive systematic literature review to identify different cell types and their functions at the human maternal-fetal interface, focusing on all original scRNAseq studies on placentas published before March 2023 and published reviews (total of 28 studies identified) using PubMed search. Our approach involved curating cell types and subtypes that had previously been defined using scRNAseq and comparing the genes used as markers or identified as potential new markers. Next, we reanalyzed expression matrices from the six available scRNAseq raw datasets with cell annotations (four from first trimester and two at term), using Wilcoxon rank-sum tests to compare gene expression among studies and annotate trophoblast cell markers in both first trimester and term placentas. Furthermore, we integrated scRNAseq raw data available from 18 healthy first trimester and nine term placentas, and performed clustering and differential gene expression analysis. We further compared markers obtained with the analysis of annotated and raw datasets with the literature to obtain a common signature gene list for major placental cell types. OUTCOMES Variations in the sampling site, gestational age, fetal sex, and subsequent sequencing and analysis methods were observed between the studies. Although their proportions varied, the three trophoblast types were consistently identified across all scRNAseq studies, unlike other non-trophoblast cell types. Notably, no marker genes were shared by all studies for any of the investigated cell types. Moreover, most of the newly defined markers in one study were not observed in other studies. These discrepancies were confirmed by our analysis on trophoblast cell types, where hundreds of potential marker genes were identified in each study but with little overlap across studies. From 35 461 and 23 378 cells of high quality in the first trimester and term placentas, respectively, we obtained major placental cell types, including perivascular cells that previously had not been identified in the first trimester. Importantly, our meta-analysis provides marker genes for major placental cell types based on our extensive curation. WIDER IMPLICATIONS This review and meta-analysis emphasizes the need for establishing a consensus for annotating placental cell types from scRNAseq data. The marker genes identified here can be deployed for defining human placental cell types, thereby facilitating and improving the reproducibility of trophoblast cell annotation.
Collapse
Affiliation(s)
- Emilie Derisoud
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, Stockholm, Sweden
| | - Hong Jiang
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, Stockholm, Sweden
| | - Allan Zhao
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, Stockholm, Sweden
| | - Pascale Chavatte-Palmer
- INRAE, BREED, Université Paris-Saclay, UVSQ, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d’Alfort, BREED, Maisons-Alfort, France
| | - Qiaolin Deng
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska University Hospital, Solna, Stockholm, Sweden
| |
Collapse
|
13
|
Edalat SG, Gerber R, Houtman M, Lückgen J, Teixeira RL, Palacios Cisneros MDP, Pfanner T, Kuret T, Ižanc N, Micheroli R, Polido-Pereira J, Saraiva F, Lingam S, Burki K, Burja B, Pauli C, Rotar Ž, Tomšič M, Čučnik S, Fonseca JE, Distler O, Calado Â, Romão VC, Ospelt C, Sodin-Semrl S, Robinson MD, Frank Bertoncelj M. Molecular maps of synovial cells in inflammatory arthritis using an optimized synovial tissue dissociation protocol. iScience 2024; 27:109707. [PMID: 38832018 PMCID: PMC11144743 DOI: 10.1016/j.isci.2024.109707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 02/25/2024] [Accepted: 04/06/2024] [Indexed: 06/05/2024] Open
Abstract
In this study, we optimized the dissociation of synovial tissue biopsies for single-cell omics studies and created a single-cell atlas of human synovium in inflammatory arthritis. The optimized protocol allowed consistent isolation of highly viable cells from tiny fresh synovial biopsies, minimizing the synovial biopsy drop-out rate. The synovium scRNA-seq atlas contained over 100,000 unsorted synovial cells from 25 synovial tissues affected by inflammatory arthritis, including 16 structural, 11 lymphoid, and 15 myeloid cell clusters. This synovial cell map expanded the diversity of synovial cell types/states, detected synovial neutrophils, and broadened synovial endothelial cell classification. We revealed tissue-resident macrophage subsets with proposed matrix-sensing (FOLR2+COLEC12high) and iron-recycling (LYVE1+SLC40A1+) activities and identified fibroblast subsets with proposed functions in cartilage breakdown (SOD2highSAA1+SAA2+SDC4+) and extracellular matrix remodeling (SERPINE1+COL5A3+LOXL2+). Our study offers an efficient synovium dissociation method and a reference scRNA-seq resource, that advances the current understanding of synovial cell heterogeneity in inflammatory arthritis.
Collapse
Affiliation(s)
- Sam G. Edalat
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich and University of Zurich, 8952 Schlieren, Switzerland
| | - Reto Gerber
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich and University of Zurich, 8952 Schlieren, Switzerland
- Department of Molecular Life Sciences and SIB, Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Miranda Houtman
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich and University of Zurich, 8952 Schlieren, Switzerland
| | | | - Rui Lourenço Teixeira
- Instituto de Medicina Molecular (iMM) João Lobo Antunes, Faculdade de Medicina, University of Lisbon, 1649-028 Lisbon, Portugal
- Faculdade de Medicina, University of Lisbon, 1649-028 Lisbon, Portugal
- Rheumatology Department, Hospital de Santa Maria, Lisbon Academic Medical Center, 1649-028 Lisbon, Portugal
| | | | | | - Tadeja Kuret
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich and University of Zurich, 8952 Schlieren, Switzerland
- Department of Rheumatology, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
| | - Nadja Ižanc
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich and University of Zurich, 8952 Schlieren, Switzerland
- Department of Rheumatology, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
| | - Raphael Micheroli
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich and University of Zurich, 8952 Schlieren, Switzerland
| | - Joaquim Polido-Pereira
- Instituto de Medicina Molecular (iMM) João Lobo Antunes, Faculdade de Medicina, University of Lisbon, 1649-028 Lisbon, Portugal
- Faculdade de Medicina, University of Lisbon, 1649-028 Lisbon, Portugal
- Rheumatology Department, Hospital de Santa Maria, Lisbon Academic Medical Center, 1649-028 Lisbon, Portugal
| | - Fernando Saraiva
- Instituto de Medicina Molecular (iMM) João Lobo Antunes, Faculdade de Medicina, University of Lisbon, 1649-028 Lisbon, Portugal
- Faculdade de Medicina, University of Lisbon, 1649-028 Lisbon, Portugal
- Rheumatology Department, Hospital de Santa Maria, Lisbon Academic Medical Center, 1649-028 Lisbon, Portugal
| | - Swathi Lingam
- Team PTA, BioMed X Institute, 69120 Heidelberg, Germany
| | - Kristina Burki
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich and University of Zurich, 8952 Schlieren, Switzerland
| | - Blaž Burja
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich and University of Zurich, 8952 Schlieren, Switzerland
- Department of Rheumatology, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
| | - Chantal Pauli
- Department of Pathology and Molecular Pathology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Žiga Rotar
- Department of Rheumatology, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Matija Tomšič
- Department of Rheumatology, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Saša Čučnik
- Department of Rheumatology, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
- Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - João Eurico Fonseca
- Instituto de Medicina Molecular (iMM) João Lobo Antunes, Faculdade de Medicina, University of Lisbon, 1649-028 Lisbon, Portugal
- Faculdade de Medicina, University of Lisbon, 1649-028 Lisbon, Portugal
- Rheumatology Department, Hospital de Santa Maria, Lisbon Academic Medical Center, 1649-028 Lisbon, Portugal
| | - Oliver Distler
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich and University of Zurich, 8952 Schlieren, Switzerland
| | - Ângelo Calado
- Instituto de Medicina Molecular (iMM) João Lobo Antunes, Faculdade de Medicina, University of Lisbon, 1649-028 Lisbon, Portugal
| | - Vasco C. Romão
- Instituto de Medicina Molecular (iMM) João Lobo Antunes, Faculdade de Medicina, University of Lisbon, 1649-028 Lisbon, Portugal
- Faculdade de Medicina, University of Lisbon, 1649-028 Lisbon, Portugal
- Rheumatology Department, Hospital de Santa Maria, Lisbon Academic Medical Center, 1649-028 Lisbon, Portugal
| | - Caroline Ospelt
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich and University of Zurich, 8952 Schlieren, Switzerland
| | - Snežna Sodin-Semrl
- Department of Rheumatology, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, 6000 Koper, Slovenia
| | - Mark D. Robinson
- Department of Molecular Life Sciences and SIB, Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Mojca Frank Bertoncelj
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich and University of Zurich, 8952 Schlieren, Switzerland
- Department of Molecular Life Sciences and SIB, Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| |
Collapse
|
14
|
Chai D, Wang J, Fan C, Lim JM, Wang X, Neeli P, Yu X, Young KH, Li Y. Remodeling of anti-tumor immunity with antibodies targeting a p53 mutant. J Hematol Oncol 2024; 17:45. [PMID: 38886748 PMCID: PMC11184848 DOI: 10.1186/s13045-024-01566-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 06/07/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND p53, the most frequently mutated gene in cancer, lacks effective targeted drugs. METHODS We developed monoclonal antibodies (mAbs) that target a p53 hotspot mutation E285K without cross-reactivity with wild-type p53. They were delivered using lipid nanoparticles (LNPs) that encapsulate DNA plasmids. Western blot, BLI, flow cytometry, single-cell sequencing (scRNA-seq), and other methods were employed to assess the function of mAbs in vitro and in vivo. RESULTS These LNP-pE285K-mAbs in the IgG1 format exhibited a robust anti-tumor effect, facilitating the infiltration of immune cells, including CD8+ T, B, and NK cells. scRNA-seq revealed that IgG1 reduces immune inhibitory signaling, increases MHC signaling from B cells to CD8+ T cells, and enriches anti-tumor T cell and B cell receptor profiles. The E285K-mAbs were also produced in the dimeric IgA (dIgA) format, whose anti-tumor activity depended on the polymeric immunoglobulin receptor (PIGR), a membrane Ig receptor, whereas that of IgG1 relied on TRIM21, an intracellular IgG receptor. CONCLUSIONS Targeting specific mutant epitopes using DNA-encoded and LNP-delivered mAbs represents a potential precision medicine strategy against p53 mutants in TRIM21- or PIGR-positive cancers.
Collapse
Affiliation(s)
- Dafei Chai
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA.
| | - Junhao Wang
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Chunmei Fan
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Jing-Ming Lim
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Xu Wang
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Praveen Neeli
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Xinfang Yu
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Ken H Young
- Department of Pathology, Division of Hematopathology, Duke University Medical Center, Durham, NC, USA
| | - Yong Li
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA.
| |
Collapse
|
15
|
Beliën J, Swinnen S, D'hondt R, de Juan LV, Dedoncker N, Matthys P, Bauer J, Vens C, Moylett S, Dubois B. CHIT1 at diagnosis predicts faster disability progression and reflects early microglial activation in multiple sclerosis. Nat Commun 2024; 15:5013. [PMID: 38866782 PMCID: PMC11169395 DOI: 10.1038/s41467-024-49312-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 05/30/2024] [Indexed: 06/14/2024] Open
Abstract
Multiple sclerosis (MS) is characterized by heterogeneity in disease course and prediction of long-term outcome remains a major challenge. Here, we investigate five myeloid markers - CHIT1, CHI3L1, sTREM2, GPNMB and CCL18 - in the cerebrospinal fluid (CSF) at diagnostic lumbar puncture in a longitudinal cohort of 192 MS patients. Through mixed-effects and machine learning models, we show that CHIT1 is a robust predictor for faster disability progression. Integrative analysis of 11 CSF and 26 central nervous system (CNS) parenchyma single-cell/nucleus RNA sequencing samples reveals CHIT1 to be predominantly expressed by microglia located in active MS lesions and enriched for lipid metabolism pathways. Furthermore, we find CHIT1 expression to accompany the transition from a homeostatic towards a more activated, MS-associated cell state in microglia. Neuropathological evaluation in post-mortem tissue from 12 MS patients confirms CHIT1 production by lipid-laden phagocytes in actively demyelinating lesions, already in early disease stages. Altogether, we provide a rationale for CHIT1 as an early biomarker for faster disability progression in MS.
Collapse
Affiliation(s)
- Jarne Beliën
- Laboratory for Neuroimmunology, Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Stijn Swinnen
- Laboratory for Neuroimmunology, Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven, Belgium
- Department of Neurology, University Hospitals Leuven, Leuven, Belgium
| | - Robbe D'hondt
- Department of Public Health and Primary Care, KU Leuven, Kortrijk, Belgium
- Imec research group itec, KU Leuven, Kortrijk, Belgium
| | - Laia Verdú de Juan
- Department of Neuroimmunology, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Nina Dedoncker
- Laboratory for Neuroimmunology, Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Patrick Matthys
- Laboratory of Immunobiology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Jan Bauer
- Department of Neuroimmunology, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Celine Vens
- Department of Public Health and Primary Care, KU Leuven, Kortrijk, Belgium
- Imec research group itec, KU Leuven, Kortrijk, Belgium
| | - Sinéad Moylett
- Laboratory for Neuroimmunology, Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Bénédicte Dubois
- Laboratory for Neuroimmunology, Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven, Belgium.
- Department of Neurology, University Hospitals Leuven, Leuven, Belgium.
| |
Collapse
|
16
|
Qadir MMF, Elgamal RM, Song K, Kudtarkar P, Sakamuri SS, Katakam PV, El-Dahr S, Kolls J, Gaulton KJ, Mauvais-Jarvis F. Single cell regulatory architecture of human pancreatic islets suggests sex differences in β cell function and the pathogenesis of type 2 diabetes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.11.589096. [PMID: 38645001 PMCID: PMC11030320 DOI: 10.1101/2024.04.11.589096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Biological sex affects the pathogenesis of type 2 and type 1 diabetes (T2D, T1D) including the development of β cell failure observed more often in males. The mechanisms that drive sex differences in β cell failure is unknown. Studying sex differences in islet regulation and function represent a unique avenue to understand the sex-specific heterogeneity in β cell failure in diabetes. Here, we examined sex and race differences in human pancreatic islets from up to 52 donors with and without T2D (including 37 donors from the Human Pancreas Analysis Program [HPAP] dataset) 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. In cultured islets from nondiabetic (ND) donors, in the absence of the in vivo hormonal environment, sex differences in islet cell type gene accessibility and expression predominantly involved sex chromosomes. Of particular interest were sex differences in the X-linked KDM6A and Y-linked KDM5D chromatin remodelers in female and male islet cells respectively. Islets from T2D donors exhibited similar sex differences in differentially expressed genes (DEGs) from sex chromosomes. However, in contrast to islets from ND donors, islets from T2D donors exhibited major sex differences in DEGs from autosomes. Comparing β cells from T2D and ND donors revealed that females had more DEGs from autosomes compared to male β cells. Gene set enrichment analysis of female β cell DEGs showed a suppression of oxidative phosphorylation and electron transport chain pathways, while male β cell had suppressed insulin secretion pathways. Thus, although sex-specific differences in gene accessibility and expression of cultured ND human islets predominantly affect sex chromosome genes, major differences in autosomal gene expression between sexes appear during the transition to T2D and which highlight mitochondrial failure in female β cells.
Collapse
Affiliation(s)
- Mirza Muhammad Fahd Qadir
- Section of Endocrinology and Metabolism, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
- Southeast Louisiana Veterans Health Care System, New Orleans, LA, USA
- Tulane Center of Excellence in Sex-Based Biology & Medicine, New Orleans, LA, USA
| | - Ruth M. Elgamal
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Keijing Song
- Center for Translational Research in Infection and Inflammation, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Parul Kudtarkar
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Siva S.V.P Sakamuri
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Prasad V. Katakam
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Samir El-Dahr
- Department of Pediatrics, Tulane University, School of Medicine, New Orleans, LA, USA
| | - Jay Kolls
- Center for Translational Research in Infection and Inflammation, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Kyle J. Gaulton
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Franck Mauvais-Jarvis
- Section of Endocrinology and Metabolism, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
- Southeast Louisiana Veterans Health Care System, New Orleans, LA, USA
- Tulane Center of Excellence in Sex-Based Biology & Medicine, New Orleans, LA, USA
| |
Collapse
|
17
|
Assatova B, Willim R, Trevisani C, Haskett G, Kariya KM, Chopra K, Park SR, Tolstorukov MY, McCabe SM, Duffy J, Louissaint A, Huuhtanen J, Bhattacharya D, Mustjoki S, Koh MJ, Powers F, Morgan EA, Yang L, Pinckney B, Cotton MJ, Crabbe A, Ziemba JB, Brain I, Heavican-Foral TB, Iqbal J, Nemec R, Rider AB, Ford JG, Koh MJ, Scanlan N, Feith DJ, Loughran TP, Kim WS, Choi J, Roels J, Boehme L, Putteman T, Taghon T, Barnes JA, Johnson PC, Jacobsen ED, Greenberg SA, Weinstock DM, Jain S. KLRG1 Cell Depletion as a Novel Therapeutic Strategy in Patients with Mature T-Cell Lymphoma Subtypes. Clin Cancer Res 2024; 30:2514-2530. [PMID: 38252421 PMCID: PMC11145167 DOI: 10.1158/1078-0432.ccr-23-3504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/02/2024] [Accepted: 01/18/2024] [Indexed: 01/23/2024]
Abstract
PURPOSE Develop a novel therapeutic strategy for patients with subtypes of mature T-cell and NK-cell neoplasms. EXPERIMENTAL DESIGN Primary specimens, cell lines, patient-derived xenograft models, commercially available, and proprietary anti-KLRG1 antibodies were used for screening, target, and functional validation. RESULTS Here we demonstrate that surface KLRG1 is highly expressed on tumor cells in subsets of patients with extranodal NK/T-cell lymphoma (ENKTCL), T-prolymphocytic leukemia (T-PLL), and gamma/delta T-cell lymphoma (G/D TCL). The majority of the CD8+/CD57+ or CD3-/CD56+ leukemic cells derived from patients with T- and NK-large granular lymphocytic leukemia (T-LGLL and NK-LGLL), respectively, expressed surface KLRG1. The humanized afucosylated anti-KLRG1 monoclonal antibody (mAb208) optimized for mouse in vivo use depleted KLRG1+ TCL cells by mechanisms of ADCC, ADCP, and CDC rather than apoptosis. mAb208 induced ADCC and ADCP of T-LGLL patient-derived CD8+/CD57+ cells ex vivo. mAb208 effected ADCC of subsets of healthy donor-derived KLRG1+ NK, CD4+, CD8+ Tem, and TemRA cells while sparing KLRG1- naïve and CD8+ Tcm cells. Treatment of cell line and TCL patient-derived xenografts with mAb208 or anti-CD47 mAb alone and in combination with the PI3K-δ/γ inhibitor duvelisib extended survival. The depletion of macrophages in vivo antagonized mAb208 efficacy. CONCLUSIONS Our findings suggest the potential benefit of a broader treatment strategy combining therapeutic antibodies with PI3Ki for the treatment of patients with mature T-cell and NK-cell neoplasms. See related commentary by Varma and Diefenbach, p. 2300.
Collapse
MESH Headings
- Humans
- Animals
- Mice
- Receptors, Immunologic/antagonists & inhibitors
- Receptors, Immunologic/metabolism
- Receptors, Immunologic/immunology
- Lectins, C-Type/metabolism
- Lectins, C-Type/immunology
- Lectins, C-Type/antagonists & inhibitors
- Xenograft Model Antitumor Assays
- Cell Line, Tumor
- Lymphoma, T-Cell/immunology
- Lymphoma, T-Cell/pathology
- Lymphoma, T-Cell/therapy
- Lymphoma, T-Cell/drug therapy
- Killer Cells, Natural/immunology
- Killer Cells, Natural/metabolism
- Antibodies, Monoclonal/therapeutic use
- Antibodies, Monoclonal/pharmacology
Collapse
Affiliation(s)
- Bimarzhan Assatova
- Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Robert Willim
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Christopher Trevisani
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- College of Medicine, SUNY Upstate Medical University, Syracuse, New York
| | - Garrett Haskett
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Khyati Maulik Kariya
- Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Kusha Chopra
- Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Sung Rye Park
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Sean M. McCabe
- Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Jessica Duffy
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Abner Louissaint
- Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Jani Huuhtanen
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | - Dipabarna Bhattacharya
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | - Satu Mustjoki
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | - Min Jung Koh
- School of Medicine, Georgetown University, Washington, District of Columbia
| | - Foster Powers
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota
| | - Elizabeth A. Morgan
- Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Lei Yang
- MD Anderson UTH Health Graduate School of Biomedical Sciences, Houston, Texas
| | - Brandy Pinckney
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Matthew J. Cotton
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Andrew Crabbe
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
- Department of Pathology, Akron General, Cleveland Clinic, Akron, Ohio
| | - Jessica Beth Ziemba
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Histopath, Inc, Corpus Christi, Texas
| | - Ian Brain
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Ontario, Canada
| | | | - Javeed Iqbal
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska
| | - Ronald Nemec
- Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Anna Baird Rider
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Josie Germain Ford
- Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Min Ji Koh
- Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Nora Scanlan
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - David J. Feith
- Department of Medicine, University of Virginia Cancer Center, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Thomas P. Loughran
- Department of Medicine, University of Virginia Cancer Center, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Won Seog Kim
- Department of Medicine, Sungkyunkwan University, Samsung Medical Center, Seoul, South Korea
| | - Jaehyuk Choi
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Juliette Roels
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Lena Boehme
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Tom Putteman
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Tom Taghon
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Jeffrey A. Barnes
- Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - P. Connor Johnson
- Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Eric D. Jacobsen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Steven A. Greenberg
- Harvard Medical School, Boston, Massachusetts
- Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts
| | - David M. Weinstock
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Salvia Jain
- Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| |
Collapse
|
18
|
Gardner AL, Jost TA, Brock A. Computational identification of surface markers for isolating distinct subpopulations from heterogeneous cancer cell populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.596337. [PMID: 38854060 PMCID: PMC11160629 DOI: 10.1101/2024.05.28.596337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Intratumor heterogeneity reduces treatment efficacy and complicates our understanding of tumor progression. There is a pressing need to understand the functions of heterogeneous tumor cell subpopulations within a tumor, yet biological systems to study these processes in vitro are limited. With the advent of single-cell RNA sequencing (scRNA-seq), it has become clear that some cancer cell line models include distinct subpopulations. Heterogeneous cell lines offer a unique opportunity to study the dynamics and evolution of genetically similar cancer cell subpopulations in controlled experimental settings. Here, we present clusterCleaver, a computational package that uses metrics of statistical distance to identify candidate surface markers maximally unique to transcriptomic subpopulations in scRNA-seq which may be used for FACS isolation. clusterCleaver was experimentally validated using the MDA-MB-231 and MDA-MB-436 breast cancer cell lines. ESAM and BST2/tetherin were experimentally confirmed as surface markers which identify and separate major transcriptomic subpopulations within MDA-MB-231 and MDA-MB-436 cells, respectively. clusterCleaver is a computationally efficient and experimentally validated workflow for identification and enrichment of distinct subpopulations within cell lines which paves the way for studies on the coexistence of cancer cell subpopulations in well-defined in vitro systems.
Collapse
Affiliation(s)
- Andrea L. Gardner
- Department of Biomedical Engineering, The University of Texas at Austin
| | - Tyler A. Jost
- Department of Biomedical Engineering, The University of Texas at Austin
| | - Amy Brock
- Department of Biomedical Engineering, The University of Texas at Austin
| |
Collapse
|
19
|
Mimpen JY, Ramos-Mucci L, Paul C, Kurjan A, Hulley PA, Ikwuanusi CT, Cohen CJ, Gwilym SE, Baldwin MJ, Cribbs AP, Snelling SJB. Single nucleus and spatial transcriptomic profiling of healthy human hamstring tendon. FASEB J 2024; 38:e23629. [PMID: 38742770 DOI: 10.1096/fj.202300601rrr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/03/2024] [Accepted: 04/11/2024] [Indexed: 05/16/2024]
Abstract
The molecular and cellular basis of health in human tendons remains poorly understood. Among human tendons, hamstring tendon has markedly low pathology and can provide a prototypic healthy tendon reference. The aim of this study was to determine the transcriptomes and location of all cell types in healthy hamstring tendon. Using single nucleus RNA sequencing, we profiled the transcriptomes of 10 533 nuclei from four healthy donors and identified 12 distinct cell types. We confirmed the presence of two fibroblast cell types, endothelial cells, mural cells, and immune cells, and identified cell types previously unreported in tendons, including different skeletal muscle cell types, satellite cells, adipocytes, and undefined nervous system cells. The location of these cell types within tendon was defined using spatial transcriptomics and imaging, and potential transcriptional networks and cell-cell interactions were analyzed. We demonstrate that fibroblasts have the highest number of potential cell-cell interactions in our dataset, are present throughout the tendon, and play an important role in the production and organization of extracellular matrix, thus confirming their role as key regulators of hamstring tendon homeostasis. Overall, our findings underscore the complexity of the cellular networks that underpin healthy human tendon function and the central role of fibroblasts as key regulators of hamstring tendon tissue homeostasis.
Collapse
Affiliation(s)
- Jolet Y Mimpen
- The Botnar Institute of Musculoskeletal Sciences, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Lorenzo Ramos-Mucci
- The Botnar Institute of Musculoskeletal Sciences, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Claudia Paul
- The Botnar Institute of Musculoskeletal Sciences, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Alina Kurjan
- The Botnar Institute of Musculoskeletal Sciences, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Philippa A Hulley
- The Botnar Institute of Musculoskeletal Sciences, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | | | - Carla J Cohen
- Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom of Great Britain and Northern Ireland
| | - Stephen E Gwilym
- The Botnar Institute of Musculoskeletal Sciences, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Mathew J Baldwin
- The Botnar Institute of Musculoskeletal Sciences, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Adam P Cribbs
- The Botnar Institute of Musculoskeletal Sciences, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Sarah J B Snelling
- The Botnar Institute of Musculoskeletal Sciences, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| |
Collapse
|
20
|
Reiner BC, Chehimi SN, Merkel R, Toikumo S, Berrettini WH, Kranzler HR, Sanchez-Roige S, Kember RL, Schmidt HD, Crist RC. A single-nucleus transcriptomic atlas of medium spiny neurons in the rat nucleus accumbens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.26.595949. [PMID: 38826289 PMCID: PMC11142250 DOI: 10.1101/2024.05.26.595949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Neural processing of rewarding stimuli involves several distinct regions, including the nucleus accumbens (NAc). The majority of NAc neurons are GABAergic projection neurons known as medium spiny neurons (MSNs). MSNs are broadly defined by dopamine receptor expression, but evidence suggests that a wider array of subtypes exist. To study MSN heterogeneity, we analyzed single-nucleus RNA sequencing data from the largest available rat NAc dataset. Analysis of 48,040 NAc MSN nuclei identified major populations belonging to the striosome and matrix compartments. Integration with mouse and human data indicated consistency across species and disease-relevance scoring using genome-wide association study results revealed potentially differential roles for MSN populations in substance use disorders. Additional high-resolution clustering identified 34 transcriptomically distinct subtypes of MSNs definable by a limited number of marker genes. Together, these data demonstrate the diversity of MSNs in the NAc and provide a basis for more targeted genetic manipulation of specific populations.
Collapse
|
21
|
Kotliar M, Kartashov A, Barski A. Accelerating Single-Cell Sequencing Data Analysis with SciDAP: A User-Friendly Approach. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.28.582604. [PMID: 38464095 PMCID: PMC10925325 DOI: 10.1101/2024.02.28.582604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Single-cell (sc) RNA, ATAC and Multiome sequencing became powerful tools for uncovering biological and disease mechanisms. Unfortunately, manual analysis of sc data presents multiple challenges due to large data volumes and complexity of configuration parameters. This complexity, as well as not being able to reproduce a computational environment, affects the reproducibility of analysis results. The Scientific Data Analysis Platform (https://SciDAP.com) allows biologists without computational expertise to analyze sequencing-based data using portable and reproducible pipelines written in Common Workflow Language (CWL). Our suite of computational pipelines addresses the most common needs in scRNA-Seq, scATAC-Seq and scMultiome data analysis. When executed on SciDAP, it offers a user-friendly alternative to manual data processing, eliminating the need for coding expertise. In this protocol, we describe the use of SciDAP to analyze scMultiome data. Similar approaches can be used for analysis of scRNA-Seq, scATAC-Seq and scVDJ-Seq datasets.
Collapse
Affiliation(s)
- Michael Kotliar
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | | | - Artem Barski
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
- Datirium, LLC, Cincinnati, OH, USA
| |
Collapse
|
22
|
Celik C, Lee STT, Tanoto FR, Veleba M, Kline K, Thibault G. Decoding the complexity of delayed wound healing following Enterococcus faecalis infection. eLife 2024; 13:RP95113. [PMID: 38767331 PMCID: PMC11105157 DOI: 10.7554/elife.95113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024] Open
Abstract
Wound infections are highly prevalent and can lead to delayed or failed healing, causing significant morbidity and adverse economic impacts. These infections occur in various contexts, including diabetic foot ulcers, burns, and surgical sites. Enterococcus faecalis is often found in persistent non-healing wounds, but its contribution to chronic wounds remains understudied. To address this, we employed single-cell RNA sequencing (scRNA-seq) on infected wounds in comparison to uninfected wounds in a mouse model. Examining over 23,000 cells, we created a comprehensive single-cell atlas that captures the cellular and transcriptomic landscape of these wounds. Our analysis revealed unique transcriptional and metabolic alterations in infected wounds, elucidating the distinct molecular changes associated with bacterial infection compared to the normal wound healing process. We identified dysregulated keratinocyte and fibroblast transcriptomes in response to infection, jointly contributing to an anti-inflammatory environment. Notably, E. faecalis infection prompted a premature, incomplete epithelial-mesenchymal transition in keratinocytes. Additionally, E. faecalis infection modulated M2-like macrophage polarization by inhibiting pro-inflammatory resolution in vitro, in vivo, and in our scRNA-seq atlas. Furthermore, we discovered macrophage crosstalk with neutrophils, which regulates chemokine signaling pathways, while promoting anti-inflammatory interactions with endothelial cells. Overall, our findings offer new insights into the immunosuppressive role of E. faecalis in wound infections.
Collapse
Affiliation(s)
- Cenk Celik
- School of Biological Sciences, Nanyang Technological UniversitySingaporeSingapore
| | - Stella Tue Ting Lee
- School of Biological Sciences, Nanyang Technological UniversitySingaporeSingapore
| | - Frederick Reinhart Tanoto
- Singapore Centre for Environmental Life Science Engineering, Nanyang Technological UniversitySingaporeSingapore
| | - Mark Veleba
- Singapore Centre for Environmental Life Science Engineering, Nanyang Technological UniversitySingaporeSingapore
| | - Kimberly Kline
- School of Biological Sciences, Nanyang Technological UniversitySingaporeSingapore
- Singapore Centre for Environmental Life Science Engineering, Nanyang Technological UniversitySingaporeSingapore
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of GenevaGenevaSwitzerland
| | - Guillaume Thibault
- School of Biological Sciences, Nanyang Technological UniversitySingaporeSingapore
- Mechanobiology Institute, National University of SingaporeSingaporeSingapore
| |
Collapse
|
23
|
Dzanibe S, Wilk AJ, Canny S, Ranganath T, Alinde B, Rubelt F, Huang H, Davis MM, Holmes SP, Jaspan HB, Blish CA, Gray CM. Premature skewing of T cell receptor clonality and delayed memory expansion in HIV-exposed infants. Nat Commun 2024; 15:4080. [PMID: 38744812 PMCID: PMC11093981 DOI: 10.1038/s41467-024-47955-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 04/15/2024] [Indexed: 05/16/2024] Open
Abstract
While preventing vertical HIV transmission has been very successful, HIV-exposed uninfected infants (iHEU) experience an elevated risk to infections compared to HIV-unexposed and uninfected infants (iHUU). Here we present a longitudinal multimodal analysis of infant immune ontogeny that highlights the impact of HIV/ARV exposure. Using mass cytometry, we show alterations in T cell memory differentiation between iHEU and iHUU being significant from week 15 of life. The altered memory T cell differentiation in iHEU was preceded by lower TCR Vβ clonotypic diversity and linked to TCR clonal depletion within the naïve T cell compartment. Compared to iHUU, iHEU had elevated CD56loCD16loPerforin+CD38+CD45RA+FcεRIγ+ NK cells at 1 month postpartum and whose abundance pre-vaccination were predictive of vaccine-induced pertussis and rotavirus antibody responses post 3 months of life. Collectively, HIV/ARV exposure disrupted the trajectory of innate and adaptive immunity from birth which may underlie relative vulnerability to infections in iHEU.
Collapse
Affiliation(s)
- Sonwabile Dzanibe
- Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Aaron J Wilk
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA, USA
| | - Susan Canny
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA, USA
- Division of Rheumatology, Department of Pediatrics, Seattle Children's Hospital, Seattle, WA, USA
| | - Thanmayi Ranganath
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA, USA
| | - Berenice Alinde
- Division of Immunology, Department of Biomedical Sciences, Biomedical Research Institute, Stellenbosch University, Cape Town, South Africa
| | - Florian Rubelt
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Huang Huang
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Mark M Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, School of Medicine, Stanford University, Stanford, CA, USA
| | - Susan P Holmes
- Department of Statistics, Stanford University, Stanford, CA, USA
| | - Heather B Jaspan
- Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa.
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
- Seattle Children's Research Institute and Department of Paediatrics and Global Health, University of Washington, Seattle, WA, USA.
| | - Catherine A Blish
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA, USA.
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Clive M Gray
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
- Division of Immunology, Department of Biomedical Sciences, Biomedical Research Institute, Stellenbosch University, Cape Town, South Africa.
| |
Collapse
|
24
|
Szabó D, Franke V, Bianco S, Batiuk MY, Paul EJ, Kukalev A, Pfisterer UG, Irastorza-Azcarate I, Chiariello AM, Demharter S, Zea-Redondo L, Lopez-Atalaya JP, Nicodemi M, Akalin A, Khodosevich K, Ungless MA, Winick-Ng W, Pombo A. A single dose of cocaine rewires the 3D genome structure of midbrain dopamine neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.10.593308. [PMID: 38766140 PMCID: PMC11100777 DOI: 10.1101/2024.05.10.593308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Midbrain dopamine neurons (DNs) respond to a first exposure to addictive drugs and play key roles in chronic drug usage1-3. As the synaptic and transcriptional changes that follow an acute cocaine exposure are mostly resolved within a few days4,5, the molecular changes that encode the long-term cellular memory of the exposure within DNs remain unknown. To investigate whether a single cocaine exposure induces long-term changes in the 3D genome structure of DNs, we applied Genome Architecture Mapping and single nucleus transcriptomic analyses in the mouse midbrain. We found extensive rewiring of 3D genome architecture at 24 hours past exposure which remains or worsens by 14 days, outlasting transcriptional responses. The cocaine-induced chromatin rewiring occurs at all genomic scales and affects genes with major roles in cocaine-induced synaptic changes. A single cocaine exposure triggers extensive long-lasting changes in chromatin condensation in post-synaptic and post-transcriptional regulatory genes, for example the unfolding of Rbfox1 which becomes most prominent 14 days post exposure. Finally, structurally remodeled genes are most expressed in a specific DN sub-type characterized by low expression of the dopamine auto-receptor Drd2, a key feature of highly cocaine-sensitive cells. These results reveal an important role for long-lasting 3D genome remodelling in the cellular memory of a single cocaine exposure, providing new hypotheses for understanding the inception of drug addiction and 3D genome plasticity.
Collapse
Affiliation(s)
- Dominik Szabó
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, 10115 Berlin, Germany
- Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Vedran Franke
- Bioinformatics & Omics Data Science platform, Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, 10115 Berlin, Germany
| | - Simona Bianco
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
| | - Mykhailo Y. Batiuk
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - Eleanor J. Paul
- MRC London Institute of Medical Sciences (LMS), London W12 0HS, UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Alexander Kukalev
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, 10115 Berlin, Germany
| | - Ulrich G. Pfisterer
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - Ibai Irastorza-Azcarate
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, 10115 Berlin, Germany
| | - Andrea M. Chiariello
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
| | - Samuel Demharter
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - Luna Zea-Redondo
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, 10115 Berlin, Germany
- Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Jose P. Lopez-Atalaya
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), 03550, Sant Joan d’Alacant, Spain
| | - Mario Nicodemi
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
- Berlin Institute of Health, 10178 Berlin, Germany
| | - Altuna Akalin
- Bioinformatics & Omics Data Science platform, Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, 10115 Berlin, Germany
| | - Konstantin Khodosevich
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - Mark A. Ungless
- MRC London Institute of Medical Sciences (LMS), London W12 0HS, UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Warren Winick-Ng
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, 10115 Berlin, Germany
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Toronto, Canada
| | - Ana Pombo
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, 10115 Berlin, Germany
- Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| |
Collapse
|
25
|
Saldana-Guerrero IM, Montano-Gutierrez LF, Boswell K, Hafemeister C, Poon E, Shaw LE, Stavish D, Lea RA, Wernig-Zorc S, Bozsaky E, Fetahu IS, Zoescher P, Pötschger U, Bernkopf M, Wenninger-Weinzierl A, Sturtzel C, Souilhol C, Tarelli S, Shoeb MR, Bozatzi P, Rados M, Guarini M, Buri MC, Weninger W, Putz EM, Huang M, Ladenstein R, Andrews PW, Barbaric I, Cresswell GD, Bryant HE, Distel M, Chesler L, Taschner-Mandl S, Farlik M, Tsakiridis A, Halbritter F. A human neural crest model reveals the developmental impact of neuroblastoma-associated chromosomal aberrations. Nat Commun 2024; 15:3745. [PMID: 38702304 PMCID: PMC11068915 DOI: 10.1038/s41467-024-47945-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/15/2024] [Indexed: 05/06/2024] Open
Abstract
Early childhood tumours arise from transformed embryonic cells, which often carry large copy number alterations (CNA). However, it remains unclear how CNAs contribute to embryonic tumourigenesis due to a lack of suitable models. Here we employ female human embryonic stem cell (hESC) differentiation and single-cell transcriptome and epigenome analysis to assess the effects of chromosome 17q/1q gains, which are prevalent in the embryonal tumour neuroblastoma (NB). We show that CNAs impair the specification of trunk neural crest (NC) cells and their sympathoadrenal derivatives, the putative cells-of-origin of NB. This effect is exacerbated upon overexpression of MYCN, whose amplification co-occurs with CNAs in NB. Moreover, CNAs potentiate the pro-tumourigenic effects of MYCN and mutant NC cells resemble NB cells in tumours. These changes correlate with a stepwise aberration of developmental transcription factor networks. Together, our results sketch a mechanistic framework for the CNA-driven initiation of embryonal tumours.
Collapse
Affiliation(s)
- Ingrid M Saldana-Guerrero
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
- Sheffield Institute for Nucleic Acids (SInFoNiA), School of Medicine and Population Health, The University of Sheffield, Sheffield, UK
| | | | - Katy Boswell
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
| | | | - Evon Poon
- Division of Clinical Studies, The Institute of Cancer Research (ICR) & Royal Marsden NHS Trust, London, UK
| | - Lisa E Shaw
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Dylan Stavish
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
| | - Rebecca A Lea
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
| | - Sara Wernig-Zorc
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Eva Bozsaky
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Irfete S Fetahu
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- Medical University of Vienna, Department of Neurology, Division of Neuropathology and Neurochemistry, Vienna, Austria
| | - Peter Zoescher
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Ulrike Pötschger
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Marie Bernkopf
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- Labdia Labordiagnostik GmbH, Vienna, Austria
| | | | - Caterina Sturtzel
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Celine Souilhol
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
- Biomolecular Sciences Research Centre, Department of Biosciences and Chemistry, Sheffield Hallam University, Sheffield, UK
| | - Sophia Tarelli
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
| | - Mohamed R Shoeb
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Polyxeni Bozatzi
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Magdalena Rados
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Maria Guarini
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Michelle C Buri
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Wolfgang Weninger
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Eva M Putz
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Miller Huang
- Children's Hospital Los Angeles, Cancer and Blood Disease Institutes, and The Saban Research Institute, Los Angeles, CA, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ruth Ladenstein
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Peter W Andrews
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
| | - Ivana Barbaric
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
| | | | - Helen E Bryant
- Sheffield Institute for Nucleic Acids (SInFoNiA), School of Medicine and Population Health, The University of Sheffield, Sheffield, UK
| | - Martin Distel
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Louis Chesler
- Division of Clinical Studies, The Institute of Cancer Research (ICR) & Royal Marsden NHS Trust, London, UK
| | | | - Matthias Farlik
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Anestis Tsakiridis
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK.
- Neuroscience Institute, The University of Sheffield, Sheffield, UK.
| | | |
Collapse
|
26
|
Rahimzadeh N, Srinivasan SS, Zhang J, Swarup V. Gene networks and systems biology in Alzheimer's disease: Insights from multi-omics approaches. Alzheimers Dement 2024; 20:3587-3605. [PMID: 38534018 PMCID: PMC11095483 DOI: 10.1002/alz.13790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/25/2024] [Accepted: 02/17/2024] [Indexed: 03/28/2024]
Abstract
Despite numerous studies in the field of dementia and Alzheimer's disease (AD), a comprehensive understanding of this devastating disease remains elusive. Bulk transcriptomics have provided insights into the underlying genetic factors at a high level. Subsequent technological advancements have focused on single-cell omics, encompassing techniques such as single-cell RNA sequencing and epigenomics, enabling the capture of RNA transcripts and chromatin states at a single cell or nucleus resolution. Furthermore, the emergence of spatial omics has allowed the study of gene responses in the vicinity of amyloid beta plaques or across various brain regions. With the vast amount of data generated, utilizing gene regulatory networks to comprehensively study this disease has become essential. This review delves into some techniques employed in the field of AD, explores the discoveries made using these techniques, and provides insights into the future of the field.
Collapse
Affiliation(s)
- Negin Rahimzadeh
- Mathematical, Computational, and Systems Biology (MCSB) ProgramUniversity of California IrvineIrvineCaliforniaUSA
| | - Shushrruth Sai Srinivasan
- Mathematical, Computational, and Systems Biology (MCSB) ProgramUniversity of California IrvineIrvineCaliforniaUSA
| | - Jing Zhang
- Department of Computer ScienceUniversity of CaliforniaIrvineCaliforniaUSA
| | - Vivek Swarup
- Department of Neurobiology and BehaviorUniversity of California IrvineIrvineCaliforniaUSA
- Institute for Memory Impairments and Neurological Disorders (MIND)University of California IrvineIrvineCaliforniaUSA
| |
Collapse
|
27
|
Vornholt E, Liharska LE, Cheng E, Hashemi A, Park YJ, Ziafat K, Wilkins L, Silk H, Linares LM, Thompson RC, Sullivan B, Moya E, Nadkarni GN, Sebra R, Schadt EE, Kopell BH, Charney AW, Beckmann ND. Characterizing cell type specific transcriptional differences between the living and postmortem human brain. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.01.24306590. [PMID: 38746297 PMCID: PMC11092720 DOI: 10.1101/2024.05.01.24306590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Single-nucleus RNA sequencing (snRNA-seq) is often used to define gene expression patterns characteristic of brain cell types as well as to identify cell type specific gene expression signatures of neurological and mental illnesses in postmortem human brains. As methods to obtain brain tissue from living individuals emerge, it is essential to characterize gene expression differences associated with tissue originating from either living or postmortem subjects using snRNA-seq, and to assess whether and how such differences may impact snRNA-seq studies of brain tissue. To address this, human prefrontal cortex single nuclei gene expression was generated and compared between 31 samples from living individuals and 21 postmortem samples. The same cell types were consistently identified in living and postmortem nuclei, though for each cell type, a large proportion of genes were differentially expressed between samples from postmortem and living individuals. Notably, estimation of cell type proportions by cell type deconvolution of pseudo-bulk data was found to be more accurate in samples from living individuals. To allow for future integration of living and postmortem brain gene expression, a model was developed that quantifies from gene expression data the probability a human brain tissue sample was obtained postmortem. These probabilities are established as a means to statistically account for the gene expression differences between samples from living and postmortem individuals. Together, the results presented here provide a deep characterization of both differences between snRNA-seq derived from samples from living and postmortem individuals, as well as qualify and account for their effect on common analyses performed on this type of data.
Collapse
|
28
|
Thompson JM, Watts SW, Terrian L, Contreras GA, Rockwell C, Rendon CJ, Wabel E, Lockwood L, Bhattacharya S, Nault R. A cell atlas of thoracic aortic perivascular adipose tissue: a focus on mechanotransducers. Am J Physiol Heart Circ Physiol 2024; 326:H1252-H1265. [PMID: 38517229 DOI: 10.1152/ajpheart.00040.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/05/2024] [Accepted: 03/13/2024] [Indexed: 03/23/2024]
Abstract
Perivascular adipose tissue (PVAT) is increasingly recognized for its function in mechanotransduction. However, major gaps remain in our understanding of the cells present in PVAT, as well as how different cells contribute to mechanotransduction. We hypothesized that snRNA-seq would reveal the expression of mechanotransducers, and test one (PIEZO1) to illustrate the expression and functional agreement between single-nuclei RNA sequencing (snRNA-seq) and physiological measurements. To contrast two brown tissues, subscapular brown adipose tissue (BAT) was also examined. We used snRNA-seq of the thoracic aorta PVAT (taPVAT) and BAT from male Dahl salt-sensitive (Dahl SS) rats to investigate cell-specific expression mechanotransducers. Localization and function of the mechanostransducer PIEZO1 were further examined using immunohistochemistry (IHC) and RNAscope, as well as pharmacological antagonism. Approximately 30,000 nuclei from taPVAT and BAT each were characterized by snRNA-seq, identifying eight major cell types expected and one unexpected (nuclei with oligodendrocyte marker genes). Cell-specific differential gene expression analysis between taPVAT and BAT identified up to 511 genes (adipocytes) with many (≥20%) being unique to individual cell types. Piezo1 was the most highly, widely expressed mechanotransducer. The presence of PIEZO1 in the PVAT but not the adventitia was confirmed by RNAscope and IHC in male and female rats. Importantly, antagonism of PIEZO1 by GsMTX4 impaired the PVAT's ability to hold tension. Collectively, the cell compositions of taPVAT and BAT are highly similar, and PIEZO1 is likely a mechanotransducer in taPVAT.NEW & NOTEWORTHY This study describes the atlas of cells in the thoracic aorta perivascular adipose tissue (taPVAT) of the Dahl-SS rat, an important hypertension model. We show that mechanotransducers are widely expressed in these cells. Moreover, PIEZO1 expression is shown to be restricted to the taPVAT and is functionally implicated in stress relaxation. These data will serve as the foundation for future studies investigating the role of taPVAT in this model of hypertensive disease.
Collapse
Affiliation(s)
- Janice M Thompson
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan, United States
| | - Stephanie W Watts
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan, United States
| | - Leah Terrian
- Department of Biomedical Engineering, Michigan State University, East Lansing, Michigan, United States
| | - G Andres Contreras
- Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, Michigan, United States
| | - Cheryl Rockwell
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan, United States
| | - C Javier Rendon
- Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, Michigan, United States
| | - Emma Wabel
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan, United States
| | - Lizbeth Lockwood
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan, United States
| | - Sudin Bhattacharya
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan, United States
- Department of Biomedical Engineering, Michigan State University, East Lansing, Michigan, United States
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, Michigan, United States
- Institute for Integrative Toxicology, Michigan State University, East Lansing, Michigan, United States
| | - Rance Nault
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan, United States
- Institute for Integrative Toxicology, Michigan State University, East Lansing, Michigan, United States
| |
Collapse
|
29
|
Gaur P, Bryois J, Calini D, Foo L, Hoozemans JJM, Malhotra D, Menon V. Single-nucleus and spatial transcriptomic profiling of human temporal cortex and white matter reveals novel associations with AD pathology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.23.590816. [PMID: 38712204 PMCID: PMC11071354 DOI: 10.1101/2024.04.23.590816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder with complex pathological manifestations and is the leading cause of cognitive decline and dementia in elderly individuals. A major goal in AD research is to identify new therapeutic pathways by studying the molecular and cellular changes in the disease, either downstream or upstream of the pathological hallmarks. In this study, we present a comprehensive investigation of cellular heterogeneity from the temporal cortex region of 40 individuals, comprising healthy donors and individuals with differing tau and amyloid burden. Using single-nucleus transcriptome analysis of 430,271 nuclei from both gray and white matter of these individuals, we identified cell type-specific subclusters in both neuronal and glial cell types with varying degrees of association with AD pathology. In particular, these associations are present in layer specific glutamatergic (excitatory) neuronal types, along with GABAergic (inhibitory) neurons and glial subtypes. These associations were observed in early as well as late pathological progression. We extended this analysis by performing multiplexed in situ hybridization using the CARTANA platform, capturing 155 genes in 13 individuals with varying levels of tau pathology. By modeling the spatial distribution of these genes and their associations with the pathology, we not only replicated key findings from our snRNA data analysis, but also identified a set of cell type-specific genes that show selective enrichment or depletion near pathological inclusions. Together, our findings allow us to prioritize specific cell types and pathways for targeted interventions at various stages of pathological progression in AD.
Collapse
Affiliation(s)
- Pallavi Gaur
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, NY, USA
| | - Julien Bryois
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases, Roche Innovation Center, CH-4070, Basel, Switzerland
| | - Daniela Calini
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases, Roche Innovation Center, CH-4070, Basel, Switzerland
| | - Lynette Foo
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases, Roche Innovation Center, CH-4070, Basel, Switzerland
| | - Jeroen J M Hoozemans
- Department of Pathology, Amsterdam Neuroscience, Amsterdam UMC, Amsterdam, Netherlands
| | - Dheeraj Malhotra
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases, Roche Innovation Center, CH-4070, Basel, Switzerland
- MS Research Unit, Biogen, Cambridge, MA, USA
| | - Vilas Menon
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, NY, USA
| |
Collapse
|
30
|
Licón-Muñoz Y, Avalos V, Subramanian S, Granger B, Martinez F, Varela S, Moore D, Perkins E, Kogan M, Berto S, Chohan M, Bowers C, Piccirillo S. Single-nucleus and spatial landscape of the sub-ventricular zone in human glioblastoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.24.590852. [PMID: 38712234 PMCID: PMC11071523 DOI: 10.1101/2024.04.24.590852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The sub-ventricular zone (SVZ) is the most well-characterized neurogenic area in the mammalian brain. We previously showed that in 65% of patients with glioblastoma (GBM), the SVZ is a reservoir of cancer stem-like cells that contribute to treatment resistance and emergence of recurrence. Here, we built a single-nucleus RNA-sequencing-based microenvironment landscape of the tumor mass (T_Mass) and the SVZ (T_SVZ) of 15 GBM patients and 2 histologically normal SVZ (N_SVZ) samples as controls. We identified a mesenchymal signature in the T_SVZ of GBM patients: tumor cells from the T_SVZ relied on the ZEB1 regulatory network, whereas tumor cells in the T_Mass relied on the TEAD1 regulatory network. Moreover, the T_SVZ microenvironment was predominantly characterized by tumor-supportive microglia, which spatially co-exist and establish heterotypic interactions with tumor cells. Lastly, differential gene expression analyses, predictions of ligand-receptor and incoming/outgoing interactions, and functional assays revealed that the IL-1β/IL-1RAcP and Wnt-5a/Frizzled-3 pathways are therapeutic targets in the T_SVZ microenvironment. Our data provide insights into the biology of the SVZ in GBM patients and identify specific targets of this microenvironment.
Collapse
Affiliation(s)
- Y. Licón-Muñoz
- The Brain Tumor Translational Laboratory, Department of Cell Biology and Physiology, University of New Mexico Health Sciences Center, Albuquerque, NM
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM
| | - V. Avalos
- The Brain Tumor Translational Laboratory, Department of Cell Biology and Physiology, University of New Mexico Health Sciences Center, Albuquerque, NM
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM
| | - S. Subramanian
- Bioinformatics Core, Department of Neuroscience, Medical University of South Carolina, Charleston, SC
- Neurogenomics Laboratory, Department of Neuroscience, Medical University of South Carolina, Charleston, SC
| | - B. Granger
- Bioinformatics Core, Department of Neuroscience, Medical University of South Carolina, Charleston, SC
- Neurogenomics Laboratory, Department of Neuroscience, Medical University of South Carolina, Charleston, SC
| | - F. Martinez
- The Brain Tumor Translational Laboratory, Department of Cell Biology and Physiology, University of New Mexico Health Sciences Center, Albuquerque, NM
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM
| | - S. Varela
- University of New Mexico School of Medicine, Albuquerque, NM
| | - D. Moore
- Bioinformatics Core, Department of Neuroscience, Medical University of South Carolina, Charleston, SC
- Neurogenomics Laboratory, Department of Neuroscience, Medical University of South Carolina, Charleston, SC
| | - E. Perkins
- Department of Neurosurgery, University of Mississippi Medical Center, Jackson, MS
| | - M. Kogan
- Department of Neurosurgery, University of New Mexico Hospital, Albuquerque, NM
| | - S. Berto
- Bioinformatics Core, Department of Neuroscience, Medical University of South Carolina, Charleston, SC
- Neurogenomics Laboratory, Department of Neuroscience, Medical University of South Carolina, Charleston, SC
| | - M.O. Chohan
- Department of Neurosurgery, University of Mississippi Medical Center, Jackson, MS
| | - C.A. Bowers
- Department of Neurosurgery, University of New Mexico Hospital, Albuquerque, NM
| | - S.G.M. Piccirillo
- The Brain Tumor Translational Laboratory, Department of Cell Biology and Physiology, University of New Mexico Health Sciences Center, Albuquerque, NM
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM
| |
Collapse
|
31
|
Rade M, Grieb N, Weiss R, Sia J, Fischer L, Born P, Boldt A, Fricke S, Franz P, Scolnick J, Venkatraman L, Xu S, Kloetzer C, Heyn S, Kubasch AS, Baber R, Wang SY, Bach E, Hoffmann S, Ussmann J, Schetschorke B, Hell S, Schwind S, Metzeler KH, Herling M, Jentzsch M, Franke GN, Sack U, Köhl U, Platzbecker U, Reiche K, Vucinic V, Merz M. Single-cell multiomic dissection of response and resistance to chimeric antigen receptor T cells against BCMA in relapsed multiple myeloma. NATURE CANCER 2024:10.1038/s43018-024-00763-8. [PMID: 38641734 DOI: 10.1038/s43018-024-00763-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 03/26/2024] [Indexed: 04/21/2024]
Abstract
Markers that predict response and resistance to chimeric antigen receptor (CAR) T cells in relapsed/refractory multiple myeloma are currently missing. We subjected mononuclear cells isolated from peripheral blood and bone marrow before and after the application of approved B cell maturation antigen-directed CAR T cells to single-cell multiomic analyses to identify markers associated with resistance and early relapse. Differences between responders and nonresponders were identified at the time of leukapheresis. Nonresponders showed an immunosuppressive microenvironment characterized by increased numbers of monocytes expressing the immune checkpoint molecule CD39 and suppressed CD8+ T cell and natural killer cell function. Analysis of CAR T cells showed cytotoxic and exhausted phenotypes in hyperexpanded clones compared to low/intermediate expanded clones. We identified potential immunotherapy targets on CAR T cells, like PD1, to improve their functionality and durability. Our work provides evidence that an immunosuppressive microenvironment causes resistance to CAR T cell therapies in multiple myeloma.
Collapse
Affiliation(s)
- Michael Rade
- Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
| | - Nora Grieb
- Department of Hematology, Cellular Therapy and Hemostaseology, University Hospital of Leipzig, Leipzig, Germany
- Innovation Center Computer Assisted Surgery, University Hospital of Leipzig, Leipzig, Germany
| | - Ronald Weiss
- Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
- Institute for Clinical Immunology, University Hospital of Leipzig, Leipzig, Germany
| | - Jaren Sia
- Singleron Biotechnologies, Cologne, Germany
| | - Luise Fischer
- Department of Hematology, Cellular Therapy and Hemostaseology, University Hospital of Leipzig, Leipzig, Germany
| | - Patrick Born
- Department of Hematology, Cellular Therapy and Hemostaseology, University Hospital of Leipzig, Leipzig, Germany
| | - Andreas Boldt
- Institute for Clinical Immunology, University Hospital of Leipzig, Leipzig, Germany
| | - Stephan Fricke
- Institute for Clinical Immunology, University Hospital of Leipzig, Leipzig, Germany
| | - Paul Franz
- Institute for Clinical Immunology, University Hospital of Leipzig, Leipzig, Germany
| | | | | | - Stacy Xu
- Singleron Biotechnologies, Cologne, Germany
| | - Christina Kloetzer
- Department of Hematology, Cellular Therapy and Hemostaseology, University Hospital of Leipzig, Leipzig, Germany
| | - Simone Heyn
- Department of Hematology, Cellular Therapy and Hemostaseology, University Hospital of Leipzig, Leipzig, Germany
| | - Anne Sophie Kubasch
- Department of Hematology, Cellular Therapy and Hemostaseology, University Hospital of Leipzig, Leipzig, Germany
| | - Ronny Baber
- Institute for Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
- Leipzig Medical Biobank, University Leipzig, Leipzig, Germany
| | - Song Yau Wang
- Department of Hematology, Cellular Therapy and Hemostaseology, University Hospital of Leipzig, Leipzig, Germany
| | - Enrica Bach
- Department of Hematology, Cellular Therapy and Hemostaseology, University Hospital of Leipzig, Leipzig, Germany
| | - Sandra Hoffmann
- Department of Hematology, Cellular Therapy and Hemostaseology, University Hospital of Leipzig, Leipzig, Germany
| | - Jule Ussmann
- Department of Hematology, Cellular Therapy and Hemostaseology, University Hospital of Leipzig, Leipzig, Germany
| | - Birthe Schetschorke
- Department of Hematology, Cellular Therapy and Hemostaseology, University Hospital of Leipzig, Leipzig, Germany
| | - Saskia Hell
- Department of Hematology, Cellular Therapy and Hemostaseology, University Hospital of Leipzig, Leipzig, Germany
| | - Sebastian Schwind
- Department of Hematology, Cellular Therapy and Hemostaseology, University Hospital of Leipzig, Leipzig, Germany
| | - Klaus H Metzeler
- Department of Hematology, Cellular Therapy and Hemostaseology, University Hospital of Leipzig, Leipzig, Germany
| | - Marco Herling
- Department of Hematology, Cellular Therapy and Hemostaseology, University Hospital of Leipzig, Leipzig, Germany
| | - Madlen Jentzsch
- Department of Hematology, Cellular Therapy and Hemostaseology, University Hospital of Leipzig, Leipzig, Germany
| | - Georg-Nikolaus Franke
- Department of Hematology, Cellular Therapy and Hemostaseology, University Hospital of Leipzig, Leipzig, Germany
| | - Ulrich Sack
- Institute for Clinical Immunology, University Hospital of Leipzig, Leipzig, Germany
| | - Ulrike Köhl
- Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
- Institute for Clinical Immunology, University Hospital of Leipzig, Leipzig, Germany
| | - Uwe Platzbecker
- Department of Hematology, Cellular Therapy and Hemostaseology, University Hospital of Leipzig, Leipzig, Germany
| | - Kristin Reiche
- Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
- Institute for Clinical Immunology, University Hospital of Leipzig, Leipzig, Germany
- Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI), Dresden, Leipzig, Germany
| | - Vladan Vucinic
- Department of Hematology, Cellular Therapy and Hemostaseology, University Hospital of Leipzig, Leipzig, Germany
| | - Maximilian Merz
- Department of Hematology, Cellular Therapy and Hemostaseology, University Hospital of Leipzig, Leipzig, Germany.
| |
Collapse
|
32
|
Gao F, Lin W, Wang X, Liao M, Zhang M, Qin N, Chen X, Xia L, Chen Q, Sha O. Identification of receptors and factors associated with human coronaviruses in the oral cavity using single-cell RNA sequencing. Heliyon 2024; 10:e28280. [PMID: 38560173 PMCID: PMC10981076 DOI: 10.1016/j.heliyon.2024.e28280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 03/12/2024] [Accepted: 03/15/2024] [Indexed: 04/04/2024] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) ravaged the world, and Coronavirus Disease 2019 (COVID-19) exhibited highly prevalent oral symptoms that had significantly impacted the lives of affected patients. However, the involvement of four human coronavirus (HCoVs), namely SARS-CoV-2, SARS-CoV, MERS-CoV, and HCoV-229E, in oral cavity infections remained poorly understood. We integrated single-cell RNA sequencing (scRNA-seq) data of seven human oral tissues through consistent normalization procedure, including minor salivary gland (MSG), parotid gland (PG), tongue, gingiva, buccal, periodontium and pulp. The Seurat, scDblFinder, Harmony, SingleR, Ucell and scCancer packages were comprehensively used for analysis. We identified specific cell clusters and generated expression profiles of SARS-CoV-2 and coronavirus-associated receptors and factors (SCARFs) in seven oral regions, providing direction for predicting the tropism of four HCoVs for oral tissues, as well as for dental clinical treatment. Based on our analysis, it appears that various SCARFs, including ACE2, ASGR1, KREMEN1, DPP4, ANPEP, CD209, CLEC4G/M, TMPRSS family proteins (including TMPRSS2, TMPRSS4, and TMPRSS11A), and FURIN, are expressed at low levels in the oral cavity. Conversely, BSG, CTSB, and CTSL exhibit enrichment in oral tissues. Our study also demonstrates widespread expression of restriction factors, particularly IFITM1-3 and LY6E, in oral cells. Additionally, some replication, assembly, and trafficking factors appear to exhibit broad oral tissues expression patterns. Overall, the oral cavity could potentially serve as a high-risk site for SARS-CoV-2 infection, while displaying a comparatively lower degree of susceptibility towards other HCoVs (including SARS-CoV, MERS-CoV and HCoV-229E). Specifically, MSG, tongue, and gingiva represent potential sites of vulnerability for four HCoVs infection, with the MSG exhibiting a particularly high susceptibility. However, the expression patterns of SCARFs in other oral sites demonstrate relatively intricate and may only be specifically associated with SARS-CoV-2 infection. Our study sheds light on the mechanisms of HCoVs infection in the oral cavity as well as gains insight into the characteristics and distribution of possible HCoVs target cells in oral tissues, providing potential therapeutic targets for HCoVs infection in the oral cavity.
Collapse
Affiliation(s)
- Feng Gao
- School of Dentistry, Shenzhen University Medical School, Shenzhen University, Shenzhen, China
- Institute of Dental Research, Shenzhen University, Shenzhen, China
| | - Weiming Lin
- Shenzhen University Medical School, Shenzhen University, Shenzhen, China
| | - Xia Wang
- Shenzhen University Medical School, Shenzhen University, Shenzhen, China
- The Chinese University of Hong Kong Shenzhen, School of Medicine, Shenzhen, China
| | - Mingfeng Liao
- The Third People's Hospital of Shenzhen, Shenzhen, China
| | - Mingxia Zhang
- The Third People's Hospital of Shenzhen, Shenzhen, China
| | - Nianhong Qin
- Department of Stomatology, Shenzhen People's Hospital, Shenzhen, China
| | - Xianxiong Chen
- School of Dentistry, Shenzhen University Medical School, Shenzhen University, Shenzhen, China
| | - Lixin Xia
- Shenzhen University Medical School, Shenzhen University, Shenzhen, China
| | - Qianming Chen
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Clinical Research Center for Oral Diseases of Zhejiang Province, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou, China
| | - Ou Sha
- School of Dentistry, Shenzhen University Medical School, Shenzhen University, Shenzhen, China
- Institute of Dental Research, Shenzhen University, Shenzhen, China
| |
Collapse
|
33
|
Neavin D, Senabouth A, Arora H, Lee JTH, Ripoll-Cladellas A, Franke L, Prabhakar S, Ye CJ, McCarthy DJ, Melé M, Hemberg M, Powell JE. Demuxafy: improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods. Genome Biol 2024; 25:94. [PMID: 38622708 PMCID: PMC11020463 DOI: 10.1186/s13059-024-03224-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 03/25/2024] [Indexed: 04/17/2024] Open
Abstract
Recent innovations in single-cell RNA-sequencing (scRNA-seq) provide the technology to investigate biological questions at cellular resolution. Pooling cells from multiple individuals has become a common strategy, and droplets can subsequently be assigned to a specific individual by leveraging their inherent genetic differences. An implicit challenge with scRNA-seq is the occurrence of doublets-droplets containing two or more cells. We develop Demuxafy, a framework to enhance donor assignment and doublet removal through the consensus intersection of multiple demultiplexing and doublet detecting methods. Demuxafy significantly improves droplet assignment by separating singlets from doublets and classifying the correct individual.
Collapse
Affiliation(s)
- Drew Neavin
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute for Medical Research, Darlinghurst, NSW, Australia.
| | - Anne Senabouth
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute for Medical Research, Darlinghurst, NSW, Australia
| | - Himanshi Arora
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute for Medical Research, Darlinghurst, NSW, Australia
- Present address: Statewide Genomics at NSW Health Pathology, Sydney, NSW, Australia
| | | | - Aida Ripoll-Cladellas
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Catalonia, Spain
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Shyam Prabhakar
- Spatial and Single Cell Systems Domain, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
- Population and Global Health, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Republic of Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Republic of Singapore
| | - Chun Jimmie Ye
- Bakar Institute for Computational Health Sciences, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Davis J McCarthy
- Bioinformatics and Cellular Genomics, St Vincent's Institute of Medical Research, Fitzroy, Australia
- Melbourne Integrative Genomics, School of BioSciences-School of Mathematics & Statistics, Faculty of Science, University of Melbourne, Melbourne, Australia
| | - Marta Melé
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Catalonia, Spain
| | - Martin Hemberg
- Present address: The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Joseph E Powell
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute for Medical Research, Darlinghurst, NSW, Australia.
- UNSW Cellular Genomics Futures Institute, University of New South Wales, Kensington, NSW, Australia.
| |
Collapse
|
34
|
Ning L, Quan C, Wang Y, Wu Z, Yuan P, Xie N. scRNA-seq characterizing the heterogeneity of fibroblasts in breast cancer reveals a novel subtype SFRP4 + CAF that inhibits migration and predicts prognosis. Front Oncol 2024; 14:1348299. [PMID: 38686196 PMCID: PMC11056562 DOI: 10.3389/fonc.2024.1348299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 03/27/2024] [Indexed: 05/02/2024] Open
Abstract
Introduction Cancer-associated fibroblasts (CAFs) are a diverse group of cells that significantly impact the tumor microenvironment and therapeutic responses in breast cancer (BC). Despite their importance, the comprehensive profile of CAFs in BC remains to be fully elucidated. Methods To address this gap, we utilized single-cell RNA sequencing (scRNA-seq) to delineate the CAF landscape within 14 BC normal-tumor paired samples. We further corroborated our findings by analyzing several public datasets, thereby validating the newly identified CAF subtype. Additionally, we conducted coculture experiments with BC cells to assess the functional implications of this CAF subtype. Results Our scRNA-seq analysis unveiled eight distinct CAF subtypes across five tumor and six adjacent normal tissue samples. Notably, we discovered a novel subtype, designated as SFRP4+ CAFs, which was predominantly observed in normal tissues. The presence of SFRP4+ CAFs was substantiated by two independent scRNA-seq datasets and a spatial transcriptomics dataset. Functionally, SFRP4+ CAFs were found to impede BC cell migration and the epithelial-mesenchymal transition (EMT) process by secreting SFRP4, thereby modulating the WNT signaling pathway. Furthermore, we established that elevated expression levels of SFRP4+ CAF markers correlate with improved survival outcomes in BC patients, yet paradoxically, they predict a diminished response to neoadjuvant chemotherapy in cases of triple-negative breast cancer. Conclusion This investigation sheds light on the heterogeneity of CAFs in BC and introduces a novel SFRP4+ CAF subtype that hinders BC cell migration. This discovery holds promise as a potential biomarker for refined prognostic assessment and therapeutic intervention in BC.
Collapse
Affiliation(s)
- Lvwen Ning
- Biobank, Shenzhen Second People’s Hospital, First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen University, Shenzhen, China
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Chuntao Quan
- Biobank, Shenzhen Second People’s Hospital, First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen University, Shenzhen, China
| | - Yue Wang
- Biobank, Shenzhen Second People’s Hospital, First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen University, Shenzhen, China
| | - Zhijie Wu
- Biobank, Shenzhen Second People’s Hospital, First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen University, Shenzhen, China
| | - Peixiu Yuan
- College of Materials and Energy, South China Agricultural University, Guangzhou, China
| | - Ni Xie
- Biobank, Shenzhen Second People’s Hospital, First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen University, Shenzhen, China
| |
Collapse
|
35
|
Chia SB, Johnson BJ, Hu J, Vermeulen R, Chadeau-Hyam M, Guntoro F, Montgomery H, Boorgula MP, Sreekanth V, Goodspeed A, Davenport B, Pereira FV, Zaberezhnyy V, Schleicher WE, Gao D, Cadar AN, Papanicolaou M, Beheshti A, Baylin SB, Costello J, Bartley JM, Morrison TE, Aguirre-Ghiso JA, Rincon M, DeGregori J. Respiratory viral infection promotes the awakening and outgrowth of dormant metastatic breast cancer cells in lungs. RESEARCH SQUARE 2024:rs.3.rs-4210090. [PMID: 38645169 PMCID: PMC11030513 DOI: 10.21203/rs.3.rs-4210090/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Breast cancer is the second most common cancer globally. Most deaths from breast cancer are due to metastatic disease which often follows long periods of clinical dormancy1. Understanding the mechanisms that disrupt the quiescence of dormant disseminated cancer cells (DCC) is crucial for addressing metastatic progression. Infection with respiratory viruses (e.g. influenza or SARS-CoV-2) is common and triggers an inflammatory response locally and systemically2,3. Here we show that influenza virus infection leads to loss of the pro-dormancy mesenchymal phenotype in breast DCC in the lung, causing DCC proliferation within days of infection, and a greater than 100-fold expansion of carcinoma cells into metastatic lesions within two weeks. Such DCC phenotypic change and expansion is interleukin-6 (IL-6)-dependent. We further show that CD4 T cells are required for the maintenance of pulmonary metastatic burden post-influenza virus infection, in part through attenuation of CD8 cell responses in the lungs. Single-cell RNA-seq analyses reveal DCC-dependent impairment of T-cell activation in the lungs of infected mice. SARS-CoV-2 infected mice also showed increased breast DCC expansion in lungs post-infection. Expanding our findings to human observational data, we observed that cancer survivors contracting a SARS-CoV-2 infection have substantially increased risks of lung metastatic progression and cancer-related death compared to cancer survivors who did not. These discoveries underscore the significant impact of respiratory viral infections on the resurgence of metastatic cancer, offering novel insights into the interconnection between infectious diseases and cancer metastasis.
Collapse
Affiliation(s)
- Shi B Chia
- University of Colorado Anschutz Medical Campus
| | | | - Junxiao Hu
- University of Colorado Anschutz Medical Campus
| | | | - Marc Chadeau-Hyam
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, UK
| | | | | | | | | | | | | | | | | | | | - Dexiang Gao
- Biostatistics and Bioinformatics Core, University of Colorado Cancer Center
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Mitic N, Neuschulz A, Spanjaard B, Schneider J, Fresmann N, Novoselc KT, Strunk T, Münster L, Olivares-Chauvet P, Ninkovic J, Junker JP. Dissecting the spatiotemporal diversity of adult neural stem cells. Mol Syst Biol 2024; 20:321-337. [PMID: 38365956 PMCID: PMC10987636 DOI: 10.1038/s44320-024-00022-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/18/2024] Open
Abstract
Adult stem cells are important for tissue turnover and regeneration. However, in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here, we dissected the diversity of neural stem cells in the adult zebrafish brain, an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single-cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze the regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells, with some subtypes being restricted to a single brain region, while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation, with different states being involved in proliferative and non-proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for the functional manipulation of neural stem cell subtypes.
Collapse
Affiliation(s)
- Nina Mitic
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Anika Neuschulz
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
- Humboldt Universität zu Berlin, Institute for Biology, Berlin, Germany
| | - Bastiaan Spanjaard
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Julia Schneider
- Helmholtz Center Munich - German Research Center for Environmental Health, Institute of Stem Cell Research, Munich, Germany
- Biomedical Center Munich (BMC), Department of Cell Biology and Anatomy, Medical Faculty, LMU, Munich, Germany
- Graduate School of Systemic Neurosciences, LMU, Munich, Germany
| | - Nora Fresmann
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Klara Tereza Novoselc
- Helmholtz Center Munich - German Research Center for Environmental Health, Institute of Stem Cell Research, Munich, Germany
- Biomedical Center Munich (BMC), Department of Cell Biology and Anatomy, Medical Faculty, LMU, Munich, Germany
- Graduate School of Systemic Neurosciences, LMU, Munich, Germany
| | - Taraneh Strunk
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Lisa Münster
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Pedro Olivares-Chauvet
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Jovica Ninkovic
- Helmholtz Center Munich - German Research Center for Environmental Health, Institute of Stem Cell Research, Munich, Germany
- Biomedical Center Munich (BMC), Department of Cell Biology and Anatomy, Medical Faculty, LMU, Munich, Germany
| | - Jan Philipp Junker
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany.
- Charité - Universitätsmedizin Berlin, Berlin, Germany.
| |
Collapse
|
37
|
Beaulaurier J, Ly L, Duty JA, Tyer C, Stevens C, Hung CT, Sookdeo A, Drong AW, Kowdle S, Turner DJ, Juul S, Hickey S, Lee B. De novo antibody discovery in human blood from full-length single B cell transcriptomics and matching haplotyped-resolved germline assemblies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.26.586834. [PMID: 38585716 PMCID: PMC10996687 DOI: 10.1101/2024.03.26.586834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Immunoglobulin (IGH, IGK, IGL) loci in the human genome are highly polymorphic regions that encode the building blocks of the light and heavy chain IG proteins that dimerize to form antibodies. The processes of V(D)J recombination and somatic hypermutation in B cells are responsible for creating an enormous reservoir of highly specific antibodies capable of binding a vast array of possible antigens. However, the antibody repertoire is fundamentally limited by the set of variable (V), diversity (D), and joining (J) alleles present in the germline IG loci. To better understand how the germline IG haplotypes contribute to the expressed antibody repertoire, we combined genome sequencing of the germline IG loci with single-cell transcriptome sequencing of B cells from the same donor. Sequencing and assembly of the germline IG loci captured the IGH locus in a single fully-phased contig where the maternal and paternal contributions to the germline V, D, and J repertoire can be fully resolved. The B cells were collected following a measles, mumps, and rubella (MMR) vaccination, resulting in a population of cells that were activated in response to this specific immune challenge. Single-cell, full-length transcriptome sequencing of these B cells resulted in whole transcriptome characterization of each cell, as well as highly-accurate consensus sequences for the somatically rearranged and hypermutated light and heavy chain IG transcripts. A subset of antibodies synthesized based on their consensus heavy and light chain transcript sequences demonstrated binding to measles antigens and neutralization of measles live virus.
Collapse
|
38
|
Butler ML, Pervaiz N, Ypsilantis P, Wang Y, Cammasola Breda J, Mazzilli S, Nicks R, Spurlock E, Hefti MM, Huber BR, Alvarez VE, Stein TD, Campbell JD, McKee AC, Cherry JD. Repetitive head impacts induce neuronal loss and neuroinflammation in young athletes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.26.586815. [PMID: 38585925 PMCID: PMC10996668 DOI: 10.1101/2024.03.26.586815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Repetitive head impacts (RHI) sustained from contact sports are the largest risk factor for chronic traumatic encephalopathy (CTE). Currently, CTE can only be diagnosed after death and the multicellular cascade of events that trigger initial hyperphosphorylated tau (p-tau) deposition remain unclear. Further, the symptoms endorsed by young individuals with early disease are not fully explained by the extent of p-tau deposition, severely hampering development of therapeutic interventions. Here, we show that RHI exposure associates with a multicellular response in young individuals (<51 years old) prior to the onset of CTE p-tau pathology that correlates with number of years of RHI exposure. Leveraging single nucleus RNA sequencing of tissue from 8 control, 9 RHI-exposed, and 11 low stage CTE individuals, we identify SPP1+ inflammatory microglia, angiogenic and inflamed endothelial cell profiles, reactive astrocytes, and altered synaptic gene expression in excitatory and inhibitory neurons in all individuals with exposure to RHI. Surprisingly, we also observe a significant loss of cortical sulcus layer 2/3 neurons in contact sport athletes compared to controls independent of p-tau pathology. These results provide robust evidence that multiple years of RHI exposure is sufficient to induce lasting cellular alterations that may underlie p-tau deposition and help explain the early clinical symptoms observed in young former contact sport athletes. Furthermore, these data identify specific cellular responses to repetitive head impacts that may direct future identification of diagnostic and therapeutic strategies for CTE.
Collapse
Affiliation(s)
- Morgane L.M.D. Butler
- Department of Anatomy & Neurobiology, Boston University Chobanian & Avedisian School of Medicine, Boston MA, USA
- Boston University Alzheimer’s Disease and CTE Centers, Boston University Chobanian & Avedisian School of Medicine, Boston MA
| | - Nida Pervaiz
- Section of Computational Biomedicine, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston MA, USA
| | | | - Yichen Wang
- Section of Computational Biomedicine, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston MA, USA
| | - Julia Cammasola Breda
- Section of Computational Biomedicine, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston MA, USA
| | - Sarah Mazzilli
- Section of Computational Biomedicine, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston MA, USA
| | | | | | - Marco M. Hefti
- Department of Pathology, University of Iowa Health Care, Iowa City IA, USA
| | - Bertrand R. Huber
- VA Boston Healthcare System, Jamaica Plain MA, USA
- National Center for PTSD, VA Boston Healthcare System, Boston MA, USA
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston MA, USA
| | - Victor E. Alvarez
- VA Boston Healthcare System, Jamaica Plain MA, USA
- VA Bedford Healthcare System, Bedford MA, USA
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston MA, USA
| | - Thor D. Stein
- Boston University Alzheimer’s Disease and CTE Centers, Boston University Chobanian & Avedisian School of Medicine, Boston MA
- VA Boston Healthcare System, Jamaica Plain MA, USA
- VA Bedford Healthcare System, Bedford MA, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston MA, USA
| | - Joshua D. Campbell
- Section of Computational Biomedicine, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston MA, USA
| | - Ann C. McKee
- Boston University Alzheimer’s Disease and CTE Centers, Boston University Chobanian & Avedisian School of Medicine, Boston MA
- VA Boston Healthcare System, Jamaica Plain MA, USA
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston MA, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston MA, USA
| | - Jonathan D. Cherry
- Department of Anatomy & Neurobiology, Boston University Chobanian & Avedisian School of Medicine, Boston MA, USA
- Boston University Alzheimer’s Disease and CTE Centers, Boston University Chobanian & Avedisian School of Medicine, Boston MA
- VA Boston Healthcare System, Jamaica Plain MA, USA
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston MA, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston MA, USA
| |
Collapse
|
39
|
Tien JCY, Chang Y, Zhang Y, Chou J, Cheng Y, Wang X, Yang J, Mannan R, Shah P, Wang XM, Todd AJ, Eyunni S, Cheng C, Rebernick RJ, Xiao L, Bao Y, Neiswender J, Brough R, Pettitt SJ, Cao X, Miner SJ, Zhou L, Wu YM, Labanca E, Wang Y, Parolia A, Cieslik M, Robinson DR, Wang Z, Feng FY, Lord CJ, Ding K, Chinnaiyan AM. CDK12 Loss Promotes Prostate Cancer Development While Exposing Vulnerabilities to Paralog-Based Synthetic Lethality. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.20.585990. [PMID: 38562774 PMCID: PMC10983964 DOI: 10.1101/2024.03.20.585990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Biallelic loss of cyclin-dependent kinase 12 (CDK12) defines a unique molecular subtype of metastatic castration-resistant prostate cancer (mCRPC). It remains unclear, however, whether CDK12 loss per se is sufficient to drive prostate cancer development-either alone, or in the context of other genetic alterations-and whether CDK12-mutant tumors exhibit sensitivity to specific pharmacotherapies. Here, we demonstrate that tissue-specific Cdk12 ablation is sufficient to induce preneoplastic lesions and robust T cell infiltration in the mouse prostate. Allograft-based CRISPR screening demonstrated that Cdk12 loss is positively associated with Trp53 inactivation but negatively associated with Pten inactivation-akin to what is observed in human mCRPC. Consistent with this, ablation of Cdk12 in prostate organoids with concurrent Trp53 loss promotes their proliferation and ability to form tumors in mice, while Cdk12 knockout in the Pten-null prostate cancer mouse model abrogates tumor growth. Bigenic Cdk12 and Trp53 loss allografts represent a new syngeneic model for the study of androgen receptor (AR)-positive, luminal prostate cancer. Notably, Cdk12/Trp53 loss prostate tumors are sensitive to immune checkpoint blockade. Cdk12-null organoids (either with or without Trp53 co-ablation) and patient-derived xenografts from tumors with CDK12 inactivation are highly sensitive to inhibition or degradation of its paralog kinase, CDK13. Together, these data identify CDK12 as a bona fide tumor suppressor gene with impact on tumor progression and lends support to paralog-based synthetic lethality as a promising strategy for treating CDK12-mutant mCRPC.
Collapse
Affiliation(s)
- Jean Ching-Yi Tien
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yu Chang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- These authors contributed equally to this work
| | - Yuping Zhang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- These authors contributed equally to this work
| | - Jonathan Chou
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, CA, USA
- These authors contributed equally to this work
| | - Yunhui Cheng
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- These authors contributed equally to this work
| | - Xiaoju Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Jianzhang Yang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, People’s Republic of China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, College of Pharmacy, Jinan University, Guangzhou 511400, People’s Republic of China
| | - Rahul Mannan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Palak Shah
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Xiao-Ming Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Abigail J. Todd
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Sanjana Eyunni
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Caleb Cheng
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Ryan J. Rebernick
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Lanbo Xiao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yi Bao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - James Neiswender
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Rachel Brough
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Stephen J. Pettitt
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Xuhong Cao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Stephanie J. Miner
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Licheng Zhou
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, People’s Republic of China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, College of Pharmacy, Jinan University, Guangzhou 511400, People’s Republic of China
| | - Yi-Mi Wu
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Estefania Labanca
- Department of Genitourinary Medical Oncology and David H. Koch Center for Applied Research of Genitourinary Cancer, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yuzhuo Wang
- Vancouver Prostate Centre, Vancouver General Hospital and Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, V6H 3Z6, Canada
| | - Abhijit Parolia
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Marcin Cieslik
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Dan R. Robinson
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Zhen Wang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, People’s Republic of China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, College of Pharmacy, Jinan University, Guangzhou 511400, People’s Republic of China
| | - Felix Y. Feng
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, CA, USA
- Departments of Radiation Oncology and Urology, University of California, San Francisco, CA, USA
| | - Christopher J. Lord
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Ke Ding
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, People’s Republic of China
| | - Arul M. Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
- Department of Urology, University of Michigan, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Lead contact
| |
Collapse
|
40
|
Park YJ, Lu TC, Jackson T, Goodman LD, Ran L, Chen J, Liang CY, Harrison E, Ko C, Hsu AL, Yamamoto S, Qi Y, Bellen HJ, Li H. Whole organism snRNA-seq reveals systemic peripheral changes in Alzheimer's Disease fly models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.10.584317. [PMID: 38559164 PMCID: PMC10979927 DOI: 10.1101/2024.03.10.584317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Peripheral tissues become disrupted in Alzheimer's Disease (AD). However, a comprehensive understanding of how the expression of AD-associated toxic proteins, Aβ42 and Tau, in neurons impacts the periphery is lacking. Using Drosophila, a prime model organism for studying aging and neurodegeneration, we generated the Alzheimer's Disease Fly Cell Atlas (AD-FCA): whole-organism single-nucleus transcriptomes of 219 cell types from adult flies neuronally expressing human Aβ42 or Tau. In-depth analyses and functional data reveal impacts on peripheral sensory neurons by Aβ42 and on various non-neuronal peripheral tissues by Tau, including the gut, fat body, and reproductive system. This novel AD atlas provides valuable insights into potential biomarkers and the intricate interplay between the nervous system and peripheral tissues in response to AD-associated proteins.
Collapse
Affiliation(s)
- Ye-Jin Park
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
- Program in Development, Disease Models & Therapeutics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tzu-Chiao Lu
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tyler Jackson
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Program in Cancer Cell Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lindsey D Goodman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Lindsey Ran
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jiaye Chen
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chung-Yi Liang
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Erin Harrison
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christina Ko
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ao-Lin Hsu
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Internal Medicine, Division of Geriatric and Palliative Medicine, University of Michigan, Ann Arbor, MI 28109, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
- Program in Development, Disease Models & Therapeutics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yanyan Qi
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
- Program in Development, Disease Models & Therapeutics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hongjie Li
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| |
Collapse
|
41
|
López L, Morosi LG, La Terza F, Bourdely P, Rospo G, Amadio R, Piperno GM, Russo V, Volponi C, Vodret S, Joshi S, Giannese F, Lazarevic D, Germano G, Stoitzner P, Bardelli A, Dalod M, Pace L, Caronni N, Guermonprez P, Benvenuti F. Dendritic cell-targeted therapy expands CD8 T cell responses to bona-fide neoantigens in lung tumors. Nat Commun 2024; 15:2280. [PMID: 38480738 PMCID: PMC10937682 DOI: 10.1038/s41467-024-46685-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 03/06/2024] [Indexed: 03/17/2024] Open
Abstract
Cross-presentation by type 1 DCs (cDC1) is critical to induce and sustain antitumoral CD8 T cell responses to model antigens, in various tumor settings. However, the impact of cross-presenting cDC1 and the potential of DC-based therapies in tumors carrying varied levels of bona-fide neoantigens (neoAgs) remain unclear. Here we develop a hypermutated model of non-small cell lung cancer in female mice, encoding genuine MHC-I neoepitopes to study neoAgs-specific CD8 T cell responses in spontaneous settings and upon Flt3L + αCD40 (DC-therapy). We find that cDC1 are required to generate broad CD8 responses against a range of diverse neoAgs. DC-therapy promotes immunogenicity of weaker neoAgs and strongly inhibits the growth of high tumor-mutational burden (TMB) tumors. In contrast, low TMB tumors respond poorly to DC-therapy, generating mild CD8 T cell responses that are not sufficient to block progression. scRNA transcriptional analysis, immune profiling and functional assays unveil the changes induced by DC-therapy in lung tissues, which comprise accumulation of cDC1 with increased immunostimulatory properties and less exhausted effector CD8 T cells. We conclude that boosting cDC1 activity is critical to broaden the diversity of anti-tumoral CD8 T cell responses and to leverage neoAgs content for therapeutic advantage.
Collapse
Affiliation(s)
- Lucía López
- Cellular Immunology, International Centre for Genetic Engineering and Biotechnology, ICGEB, Trieste, Italy
| | - Luciano Gastón Morosi
- Cellular Immunology, International Centre for Genetic Engineering and Biotechnology, ICGEB, Trieste, Italy
| | - Federica La Terza
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Pierre Bourdely
- Université Paris Cité, Institut Cochin, INSERM 1016, Paris, France
- Laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, VIB, KU Leuven, Leuven, Belgium
| | - Giuseppe Rospo
- Department of Oncology, Molecular Biotechnology Center, University of Torino, Turin, Italy
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Roberto Amadio
- Cellular Immunology, International Centre for Genetic Engineering and Biotechnology, ICGEB, Trieste, Italy
| | - Giulia Maria Piperno
- Cellular Immunology, International Centre for Genetic Engineering and Biotechnology, ICGEB, Trieste, Italy
| | - Valentina Russo
- G. Armenise-Harvard Immune Regulation Unit, IIGM, Candiolo, TO, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, TO, Italy
| | - Camilla Volponi
- Cellular Immunology, International Centre for Genetic Engineering and Biotechnology, ICGEB, Trieste, Italy
- Cellular and Molecular Oncoimmunology, IRCCS Humanitas Research Hospital, Rozzano, Italy
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Italy
| | - Simone Vodret
- Cellular Immunology, International Centre for Genetic Engineering and Biotechnology, ICGEB, Trieste, Italy
| | - Sonal Joshi
- Cellular Immunology, International Centre for Genetic Engineering and Biotechnology, ICGEB, Trieste, Italy
| | - Francesca Giannese
- Center for Omics Sciences, IRCCS San Raffaele Institute, Milano, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Dejan Lazarevic
- Center for Omics Sciences, IRCCS San Raffaele Institute, Milano, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Giovanni Germano
- Department of Oncology, Molecular Biotechnology Center, University of Torino, Turin, Italy
- IFOM ETS - The AIRC Institute of Molecular Oncology, 20139, Milan, Italy
| | - Patrizia Stoitzner
- Department of Dermatology, Venereology & Allergology, Medical University of Innsbruck, Innsbruck, Austria
| | - Alberto Bardelli
- Department of Oncology, Molecular Biotechnology Center, University of Torino, Turin, Italy
- IFOM ETS - The AIRC Institute of Molecular Oncology, 20139, Milan, Italy
| | - Marc Dalod
- Aix-Marseille University, CNRS, INSERM, CIML, Centre d'Immunologie de Marseille-Luminy, Turing Center for Living Systems, Marseille, France
| | - Luigia Pace
- G. Armenise-Harvard Immune Regulation Unit, IIGM, Candiolo, TO, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, TO, Italy
| | - Nicoletta Caronni
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Federica Benvenuti
- Cellular Immunology, International Centre for Genetic Engineering and Biotechnology, ICGEB, Trieste, Italy.
| |
Collapse
|
42
|
Martins LR, Sieverling L, Michelhans M, Schiller C, Erkut C, Grünewald TGP, Triana S, Fröhling S, Velten L, Glimm H, Scholl C. Single-cell division tracing and transcriptomics reveal cell types and differentiation paths in the regenerating lung. Nat Commun 2024; 15:2246. [PMID: 38472236 DOI: 10.1038/s41467-024-46469-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 02/28/2024] [Indexed: 03/14/2024] Open
Abstract
Understanding the molecular and cellular processes involved in lung epithelial regeneration may fuel the development of therapeutic approaches for lung diseases. We combine mouse models allowing diphtheria toxin-mediated damage of specific epithelial cell types and parallel GFP-labeling of functionally dividing cells with single-cell transcriptomics to characterize the regeneration of the distal lung. We uncover cell types, including Krt13+ basal and Krt15+ club cells, detect an intermediate cell state between basal and goblet cells, reveal goblet cells as actively dividing progenitor cells, and provide evidence that adventitial fibroblasts act as supporting cells in epithelial regeneration. We also show that diphtheria toxin-expressing cells can persist in the lung, express specific inflammatory factors, and transcriptionally resemble a previously undescribed population in the lungs of COVID-19 patients. Our study provides a comprehensive single-cell atlas of the distal lung that characterizes early transcriptional and cellular responses to concise epithelial injury, encompassing proliferation, differentiation, and cell-to-cell interactions.
Collapse
Affiliation(s)
- Leila R Martins
- Division of Applied Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany.
| | - Lina Sieverling
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- Division of Translational Medical Oncology, DKFZ, Heidelberg, Germany
| | - Michelle Michelhans
- Division of Applied Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- Division of Translational Medical Oncology, DKFZ, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Chiara Schiller
- Division of Applied Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University Hospital and Heidelberg University, Heidelberg, Germany
| | - Cihan Erkut
- Division of Applied Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
| | - Thomas G P Grünewald
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Translational Pediatric Sarcoma Research, DKFZ, Heidelberg, Germany
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Sergio Triana
- Structural and Computational Biology, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Broad Institute of Harvard and MIT, Cambridge, USA
- Department of Chemistry, Institute for Medical Engineering and Sciences (IMES), and Koch Institute for Integrative Cancer Research, MIT, Cambridge, USA
| | - Stefan Fröhling
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- Division of Translational Medical Oncology, DKFZ, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Lars Velten
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Hanno Glimm
- Department for Translational Medical Oncology, National Center for Tumor Diseases Dresden (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Translational Functional Cancer Genomics, DKFZ, Heidelberg, Germany
- DKTK, partner site Dresden, Dresden, Germany
| | - Claudia Scholl
- Division of Applied Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany.
| |
Collapse
|
43
|
Hanhart D, Gossi F, Rapsomaniki MA, Kruithof-de Julio M, Chouvardas P. ScLinear predicts protein abundance at single-cell resolution. Commun Biol 2024; 7:267. [PMID: 38438709 PMCID: PMC10912329 DOI: 10.1038/s42003-024-05958-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 02/22/2024] [Indexed: 03/06/2024] Open
Abstract
Single-cell multi-omics have transformed biomedical research and present exciting machine learning opportunities. We present scLinear, a linear regression-based approach that predicts single-cell protein abundance based on RNA expression. ScLinear is vastly more efficient than state-of-the-art methodologies, without compromising its accuracy. ScLinear is interpretable and accurately generalizes in unseen single-cell and spatial transcriptomics data. Importantly, we offer a critical view in using complex algorithms ignoring simpler, faster, and more efficient approaches.
Collapse
Affiliation(s)
- Daniel Hanhart
- Urology Research Laboratory, Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Federico Gossi
- Urology Research Laboratory, Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | | | - Marianna Kruithof-de Julio
- Urology Research Laboratory, Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
- Department of Urology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
| | - Panagiotis Chouvardas
- Urology Research Laboratory, Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland.
- Department of Urology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland.
| |
Collapse
|
44
|
Feng S, McNehlan ME, Kinsella RL, Sur Chowdhury C, Chavez SM, Naik SK, McKee SR, Van Winkle JA, Dubey N, Samuels A, Swain A, Cui X, Hendrix SV, Woodson R, Kreamalmeyer D, Smirnov A, Artyomov MN, Virgin HW, Wang YT, Stallings CL. Autophagy promotes efficient T cell responses to restrict high-dose Mycobacterium tuberculosis infection in mice. Nat Microbiol 2024; 9:684-697. [PMID: 38413834 DOI: 10.1038/s41564-024-01608-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 01/16/2024] [Indexed: 02/29/2024]
Abstract
Although autophagy sequesters Mycobacterium tuberculosis (Mtb) in in vitro cultured macrophages, loss of autophagy in macrophages in vivo does not result in susceptibility to a standard low-dose Mtb infection until late during infection, leaving open questions regarding the protective role of autophagy during Mtb infection. Here we report that loss of autophagy in lung macrophages and dendritic cells results in acute susceptibility of mice to high-dose Mtb infection, a model mimicking active tuberculosis. Rather than observing a role for autophagy in controlling Mtb replication in macrophages, we find that autophagy suppresses macrophage responses to Mtb that otherwise result in accumulation of myeloid-derived suppressor cells and subsequent defects in T cell responses. Our finding that the pathogen-plus-susceptibility gene interaction is dependent on dose has important implications both for understanding how Mtb infections in humans lead to a spectrum of outcomes and for the potential use of autophagy modulators in clinical medicine.
Collapse
Affiliation(s)
- Siwei Feng
- Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Michael E McNehlan
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Rachel L Kinsella
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Chanchal Sur Chowdhury
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Sthefany M Chavez
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Sumanta K Naik
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Samuel R McKee
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Jacob A Van Winkle
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Neha Dubey
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Amanda Samuels
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Amanda Swain
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Xiaoyan Cui
- Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Skyler V Hendrix
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Reilly Woodson
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Darren Kreamalmeyer
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Asya Smirnov
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Maxim N Artyomov
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Herbert W Virgin
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ya-Ting Wang
- Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China.
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA.
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Shanxi Medical University, Taiyuan, Shanxi, China.
| | - Christina L Stallings
- Department of Molecular Microbiology, Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA.
| |
Collapse
|
45
|
Pereira WJ, Boyd J, Conde D, Triozzi PM, Balmant KM, Dervinis C, Schmidt HW, Boaventura-Novaes C, Chakraborty S, Knaack SA, Gao Y, Feltus FA, Roy S, Ané JM, Frugoli J, Kirst M. The single-cell transcriptome program of nodule development cellular lineages in Medicago truncatula. Cell Rep 2024; 43:113747. [PMID: 38329875 DOI: 10.1016/j.celrep.2024.113747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 10/31/2023] [Accepted: 01/22/2024] [Indexed: 02/10/2024] Open
Abstract
Legumes establish a symbiotic relationship with nitrogen-fixing rhizobia by developing nodules. Nodules are modified lateral roots that undergo changes in their cellular development in response to bacteria, but the transcriptional reprogramming that occurs in these root cells remains largely uncharacterized. Here, we describe the cell-type-specific transcriptome response of Medicago truncatula roots to rhizobia during early nodule development in the wild-type genotype Jemalong A17, complemented with a hypernodulating mutant (sunn-4) to expand the cell population responding to infection and subsequent biological inferences. The analysis identifies epidermal root hair and stele sub-cell types associated with a symbiotic response to infection and regulation of nodule proliferation. Trajectory inference shows cortex-derived cell lineages differentiating to form the nodule primordia and, posteriorly, its meristem, while modulating the regulation of phytohormone-related genes. Gene regulatory analysis of the cell transcriptomes identifies new regulators of nodulation, including STYLISH 4, for which the function is validated.
Collapse
Affiliation(s)
- Wendell J Pereira
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Jade Boyd
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Daniel Conde
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA; Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, 28223 Madrid, Spain
| | - Paolo M Triozzi
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA; PlantLab, Center of Plant Sciences, Sant'Anna School of Advanced Studies, 56010 Pisa, Italy
| | - Kelly M Balmant
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA; Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Christopher Dervinis
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Henry W Schmidt
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA
| | | | - Sanhita Chakraborty
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Sara A Knaack
- Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI 53715, USA
| | - Yueyao Gao
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Frank Alexander Feltus
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, USA; Biomedical Data Science and Informatics Program, Clemson University, Clemson, SC, USA; Clemson Center for Human Genetics, Clemson University, Greenwood, SC 29646, USA
| | - Sushmita Roy
- Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI 53715, USA; Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI 53726, USA; Department of Computer Sciences, University of Wisconsin, Madison, WI 53706, USA
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Julia Frugoli
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - Matias Kirst
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA.
| |
Collapse
|
46
|
Xu M, Li S, Xie X, Guo L, Yu D, Zhuo J, Lin J, Kol L, Gan L. ISL1 and POU4F1 Directly Interact to Regulate the Differentiation and Survival of Inner Ear Sensory Neurons. J Neurosci 2024; 44:e1718232024. [PMID: 38267260 PMCID: PMC10883659 DOI: 10.1523/jneurosci.1718-23.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 01/05/2024] [Accepted: 01/11/2024] [Indexed: 01/26/2024] Open
Abstract
The inner ear sensory neurons play a pivotal role in auditory processing and balance control. Though significant progresses have been made, the underlying mechanisms controlling the differentiation and survival of the inner ear sensory neurons remain largely unknown. During development, ISL1 and POU4F transcription factors are co-expressed and are required for terminal differentiation, pathfinding, axon outgrowth and the survival of neurons in the central and peripheral nervous systems. However, little is understood about their functional relationship and regulatory mechanism in neural development. Here, we have knocked out Isl1 or Pou4f1 or both in mice of both sexes. In the absence of Isl1, the differentiation of cochleovestibular ganglion (CVG) neurons is disturbed and with that Isl1-deficient CVG neurons display defects in migration and axon pathfinding. Compound deletion of Isl1 and Pou4f1 causes a delay in CVG differentiation and results in a more severe CVG defect with a loss of nearly all of spiral ganglion neurons (SGNs). Moreover, ISL1 and POU4F1 interact directly in developing CVG neurons and act cooperatively as well as independently in regulating the expression of unique sets of CVG-specific genes crucial for CVG development and survival by binding to the cis-regulatory elements including the promoters of Fgf10, Pou4f2, and Epha5 and enhancers of Eya1 and Ntng2 These findings demonstrate that Isl1 and Pou4f1 are indispensable for CVG development and maintenance by acting epistatically to regulate genes essential for CVG development.
Collapse
Affiliation(s)
- Mei Xu
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Department of Neuroscience and Regenerative Medicine, Augusta University, Augusta, Georgia 30912
- Institution of Life Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Shuchun Li
- Department of Neuroscience and Regenerative Medicine, Augusta University, Augusta, Georgia 30912
| | - Xiaoling Xie
- Department of Neuroscience and Regenerative Medicine, Augusta University, Augusta, Georgia 30912
| | - Luming Guo
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Department of Neuroscience and Regenerative Medicine, Augusta University, Augusta, Georgia 30912
- Institution of Life Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Dongliang Yu
- College of Life Science and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Jiaping Zhuo
- Department of Neuroscience and Regenerative Medicine, Augusta University, Augusta, Georgia 30912
| | - Jacey Lin
- Department of Neuroscience and Regenerative Medicine, Augusta University, Augusta, Georgia 30912
| | - Lotem Kol
- Department of Neuroscience and Regenerative Medicine, Augusta University, Augusta, Georgia 30912
| | - Lin Gan
- Department of Neuroscience and Regenerative Medicine, Augusta University, Augusta, Georgia 30912
- James and Jean Culver Vision Discovery Institute, Medical College of Georgia, Augusta University, Georgia 30912
| |
Collapse
|
47
|
Zhang X, Marand AP, Yan H, Schmitz RJ. Massive-scale single-cell chromatin accessibility sequencing using combinatorial fluidic indexing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.17.558155. [PMID: 37786710 PMCID: PMC10541611 DOI: 10.1101/2023.09.17.558155] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Single-cell ATAC-seq has emerged as a powerful approach for revealing candidate cis-regulatory elements genome-wide at cell-type resolution. However, current single-cell methods suffer from limited throughput and high costs. Here, we present a novel technique called single-cell combinatorial fluidic indexing ATAC-sequencing ("scifi-ATAC-seq"), which combines a barcoded Tn5 pre-indexing step with droplet-based single-cell ATAC-seq using a widely commercialized microfluidics platform (10X Genomics). With scifi-ATAC-seq, up to 200,000 nuclei across multiple samples in a single emulsion reaction can be indexed, representing a ~20-fold increase in throughput compared to the standard 10X Genomics workflow.
Collapse
Affiliation(s)
- Xuan Zhang
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Alexandre P Marand
- Department of Genetics, University of Georgia, Athens, GA, USA
- Current address: Department of Molecular, Cellular, and Development Biology, University of Michigan, Ann Arbor, MI, USA
| | - Haidong Yan
- Department of Genetics, University of Georgia, Athens, GA, USA
| | | |
Collapse
|
48
|
Gibson A, Ram R, Gangula R, Li Y, Mukherjee E, Palubinsky AM, Campbell CN, Thorne M, Konvinse KC, Choshi P, Deshpande P, Pedretti S, O’Neil RT, Wanjalla CN, Kalams SA, Gaudieri S, Lehloenya RJ, Bailin SS, Chopra A, Mallal SA, Phillips EJ. Multiomic single-cell sequencing defines tissue-specific responses in Stevens-Johnson Syndrome and Toxic epidermal necrolysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.26.568771. [PMID: 38405793 PMCID: PMC10888802 DOI: 10.1101/2023.11.26.568771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Stevens-Johnson syndrome and toxic epidermal necrolysis (SJS/TEN) is a rare but life-threatening cutaneous drug reaction mediated by human leukocyte antigen (HLA) class I-restricted CD8+ T-cells. To obtain an unbiased assessment of SJS/TEN cellular immunopathogenesis, we performed single-cell (sc) transcriptome, surface proteome, and TCR sequencing on unaffected skin, affected skin, and blister fluid from 17 SJS/TEN patients. From 119,784 total cells, we identified 16 scRNA-defined subsets, confirmed by subset-defining surface protein expression. Keratinocytes upregulated HLA and IFN-response genes in the affected skin. Cytotoxic CD8+ T-cell subpopulations of expanded and unexpanded TCRαβ clonotypes were shared in affected skin and blister fluid but absent or unexpanded in SJS/TEN unaffected skin. SJS/TEN blister fluid is a rich reservoir of oligoclonal CD8+ T-cells with an effector phenotype driving SJS/TEN pathogenesis. This multiomic database will act as the basis to define antigen-reactivity, HLA restriction, and signatures of drug-antigen-reactive T-cell clonotypes at a tissue level.
Collapse
Affiliation(s)
- Andrew Gibson
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia
| | - Ramesh Ram
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia
| | - Rama Gangula
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Yueran Li
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia
| | - Eric Mukherjee
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Amy M Palubinsky
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Chelsea N Campbell
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Michael Thorne
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia
| | - Katherine C Konvinse
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Phuti Choshi
- Allergy and Immunology Unit, University of Cape Town Lung Institute, Cape Town, South Africa
| | - Pooja Deshpande
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia
| | - Sarah Pedretti
- Allergy and Immunology Unit, University of Cape Town Lung Institute, Cape Town, South Africa
| | - Richard T O’Neil
- Department of Veterans Affairs, Ralph H Johnson VA Medical Center and Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Celestine N Wanjalla
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Spyros A Kalams
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Silvana Gaudieri
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
- School of Human Sciences, The University of Western Australia, Western Australia, Australia
| | - Rannakoe J Lehloenya
- Allergy and Immunology Unit, University of Cape Town Lung Institute, Cape Town, South Africa
- Division of Dermatology, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
| | - Samuel S Bailin
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Abha Chopra
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Jason A Trubiano on behalf of the AUS-SCAR study group
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria, Australia
- Centre for Antibiotic Allergy and Research, Department of Infectious Diseases, Austin Health, Victoria, Australia
| | | | - Simon A Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Elizabeth J Phillips
- Institute for Immunology and Infectious Diseases, Murdoch University, Western Australia, Australia
- Department of Medicine, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| |
Collapse
|
49
|
Massoni-Badosa R, Aguilar-Fernández S, Nieto JC, Soler-Vila P, Elosua-Bayes M, Marchese D, Kulis M, Vilas-Zornoza A, Bühler MM, Rashmi S, Alsinet C, Caratù G, Moutinho C, Ruiz S, Lorden P, Lunazzi G, Colomer D, Frigola G, Blevins W, Romero-Rivero L, Jiménez-Martínez V, Vidal A, Mateos-Jaimez J, Maiques-Diaz A, Ovejero S, Moreaux J, Palomino S, Gomez-Cabrero D, Agirre X, Weniger MA, King HW, Garner LC, Marini F, Cervera-Paz FJ, Baptista PM, Vilaseca I, Rosales C, Ruiz-Gaspà S, Talks B, Sidhpura K, Pascual-Reguant A, Hauser AE, Haniffa M, Prosper F, Küppers R, Gut IG, Campo E, Martin-Subero JI, Heyn H. An atlas of cells in the human tonsil. Immunity 2024; 57:379-399.e18. [PMID: 38301653 PMCID: PMC10869140 DOI: 10.1016/j.immuni.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/07/2023] [Accepted: 01/09/2024] [Indexed: 02/03/2024]
Abstract
Palatine tonsils are secondary lymphoid organs (SLOs) representing the first line of immunological defense against inhaled or ingested pathogens. We generated an atlas of the human tonsil composed of >556,000 cells profiled across five different data modalities, including single-cell transcriptome, epigenome, proteome, and immune repertoire sequencing, as well as spatial transcriptomics. This census identified 121 cell types and states, defined developmental trajectories, and enabled an understanding of the functional units of the tonsil. Exemplarily, we stratified myeloid slan-like subtypes, established a BCL6 enhancer as locally active in follicle-associated T and B cells, and identified SIX5 as putative transcriptional regulator of plasma cell maturation. Analyses of a validation cohort confirmed the presence, annotation, and markers of tonsillar cell types and provided evidence of age-related compositional shifts. We demonstrate the value of this resource by annotating cells from B cell-derived mantle cell lymphomas, linking transcriptional heterogeneity to normal B cell differentiation states of the human tonsil.
Collapse
Affiliation(s)
| | | | - Juan C Nieto
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Paula Soler-Vila
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | | | | | - Marta Kulis
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Amaia Vilas-Zornoza
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), University of Navarra, IDISNA, Universidad de Navarra, Pamplona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
| | - Marco Matteo Bühler
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland; Hematopathology Section, Pathology Department, Hospital Clinic, Barcelona, Spain
| | - Sonal Rashmi
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Clara Alsinet
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Ginevra Caratù
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Catia Moutinho
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Sara Ruiz
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Patricia Lorden
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Giulia Lunazzi
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Dolors Colomer
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain; Hematopathology Section, Pathology Department, Hospital Clinic, Barcelona, Spain; Departament de Fonaments Clínics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - Gerard Frigola
- Hematopathology Section, Pathology Department, Hospital Clinic, Barcelona, Spain
| | - Will Blevins
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Lucia Romero-Rivero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | | | - Anna Vidal
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Judith Mateos-Jaimez
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Alba Maiques-Diaz
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Sara Ovejero
- Department of Biological Hematology, CHU Montpellier, Montpellier, France; Institute of Human Genetics, UMR 9002 CNRS-UM, Montpellier, France
| | - Jérôme Moreaux
- Department of Biological Hematology, CHU Montpellier, Montpellier, France; Institute of Human Genetics, UMR 9002 CNRS-UM, Montpellier, France; Department of Clinical Hematology, CHU Montpellier, Montpellier, France
| | - Sara Palomino
- Translational Bioinformatics Unit (TransBio), Navarrabiomed, Navarra Health Department (CHN), Public University of Navarra (UPNA), Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
| | - David Gomez-Cabrero
- Translational Bioinformatics Unit (TransBio), Navarrabiomed, Navarra Health Department (CHN), Public University of Navarra (UPNA), Navarra Institute for Health Research (IdiSNA), Pamplona, Spain; Bioscience Program, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology KAUST, Thuwal, Saudi Arabia
| | - Xabier Agirre
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), University of Navarra, IDISNA, Universidad de Navarra, Pamplona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
| | - Marc A Weniger
- Institute of Cell Biology (Cancer Research), Medical Faculty, University of Duisburg-Essen, Essen, Germany
| | - Hamish W King
- Epigenetics and Development Division, Walter and Eliza Hall Institute, Parkville, Australia
| | - Lucy C Garner
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Federico Marini
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany; Center for Thrombosis and Hemostasis (CTH), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | | | - Peter M Baptista
- Department of Otorhinolaryngology, University of Navarra, Pamplona, Spain
| | - Isabel Vilaseca
- Otorhinolaryngology Head-Neck Surgery Department, Hospital Clínic, IDIBAPS Universitat de Barcelona, Barcelona, Spain
| | - Cecilia Rosales
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Silvia Ruiz-Gaspà
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Benjamin Talks
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK; Department of Otolaryngology, Freeman Hospital, Newcastle Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
| | - Keval Sidhpura
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Anna Pascual-Reguant
- Department of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany; Immune Dynamics, Deutsches Rheuma-Forschungszentrum (DRFZ), Berlin, Germany
| | - Anja E Hauser
- Department of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany; Immune Dynamics, Deutsches Rheuma-Forschungszentrum (DRFZ), Berlin, Germany
| | - Muzlifah Haniffa
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK; Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
| | - Felipe Prosper
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), University of Navarra, IDISNA, Universidad de Navarra, Pamplona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain; Departamento de Hematología, Clínica Universidad de Navarra, University of Navarra, Pamplona, Spain
| | - Ralf Küppers
- Institute of Cell Biology (Cancer Research), Medical Faculty, University of Duisburg-Essen, Essen, Germany
| | - Ivo Glynne Gut
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Elias Campo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain; Hematopathology Section, Pathology Department, Hospital Clinic, Barcelona, Spain; Departament de Fonaments Clínics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - José Ignacio Martin-Subero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Departament de Fonaments Clínics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
| | - Holger Heyn
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| |
Collapse
|
50
|
Sun J, Ruiz Daniels R, Balic A, Andresen AMS, Bjørgen H, Dobie R, Henderson NC, Koppang EO, Martin SAM, Fosse JH, Taylor RS, Macqueen DJ. Cell atlas of the Atlantic salmon spleen reveals immune cell heterogeneity and cell-specific responses to bacterial infection. FISH & SHELLFISH IMMUNOLOGY 2024; 145:109358. [PMID: 38176627 DOI: 10.1016/j.fsi.2024.109358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/23/2023] [Accepted: 01/02/2024] [Indexed: 01/06/2024]
Abstract
The spleen is a conserved secondary lymphoid organ that emerged in parallel to adaptive immunity in early jawed vertebrates. Recent studies have applied single cell transcriptomics to reveal the cellular composition of spleen in several species, cataloguing diverse immune cell types and subpopulations. In this study, 51,119 spleen nuclei transcriptomes were comprehensively investigated in the commercially important teleost Atlantic salmon (Salmo salar L.), contrasting control animals with those challenged with the bacterial pathogen Aeromonas salmonicida. We identified clusters of nuclei representing the expected major cell types, namely T cells, B cells, natural killer-like cells, granulocytes, mononuclear phagocytes, endothelial cells, mesenchymal cells, erythrocytes and thrombocytes. We discovered heterogeneity within several immune lineages, providing evidence for resident macrophages and melanomacrophages, infiltrating monocytes, several candidate dendritic cell subpopulations, and B cells at distinct stages of differentiation, including plasma cells and an igt + subset. We provide evidence for twelve candidate T cell subsets, including cd4+ T helper and regulatory T cells, one cd8+ subset, three γδT subsets, and populations double negative for cd4 and cd8. The number of genes showing differential expression during the early stages of Aeromonas infection was highly variable across immune cell types, with the largest changes observed in macrophages and infiltrating monocytes, followed by resting mature B cells. Our analysis provides evidence for a local inflammatory response to infection alongside B cell maturation in the spleen, and upregulation of ccr9 genes in igt + B cells, T helper and cd8+ cells, and monocytes, consistent with the recruitment of immune cell populations to the gut to deal with Aeromonas infection. Overall, this study provides a new cell-resolved perspective of the immune actions of Atlantic salmon spleen, highlighting extensive heterogeneity hidden to bulk transcriptomics. We further provide a large catalogue of cell-specific marker genes that can be leveraged to further explore the function and structural organization of the salmonid immune system.
Collapse
Affiliation(s)
- Jianxuan Sun
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - Rose Ruiz Daniels
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - Adam Balic
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK; Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | | | - Håvard Bjørgen
- Unit of Anatomy, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Ross Dobie
- Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, UK
| | - Neil C Henderson
- Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, UK; MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Erling Olaf Koppang
- Unit of Anatomy, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Samuel A M Martin
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | | | - Richard S Taylor
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - Daniel J Macqueen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK.
| |
Collapse
|