Learning single-cell perturbation responses using neural optimal transport

Nature Methods, Год журнала: 2023, Номер 20(11), С. 1759 - 1768

Опубликована: Сен. 28, 2023

Abstract Understanding and predicting molecular responses in single cells upon chemical, genetic or mechanical perturbations is a core question biology. Obtaining single-cell measurements typically requires the to be destroyed. This makes learning heterogeneous perturbation challenging as we only observe unpaired distributions of perturbed non-perturbed cells. Here leverage theory optimal transport recent advent input convex neural architectures present CellOT, framework for response individual given by mapping these distributions. CellOT outperforms current methods at drug responses, profiled scRNA-seq multiplexed protein-imaging technology. Further, illustrate that generalizes well on unseen settings (1) holdout patients with lupus exposed interferon-β glioblastoma panobinostat; (2) inferring lipopolysaccharide across different species; (3) modeling hematopoietic developmental trajectories subpopulations.

Язык: Английский

---

Multimodal characterization of murine gastruloid development

Cell stem cell, Год журнала: 2023, Номер 30(6), С. 867 - 884.e11

Опубликована: Май 19, 2023

Gastruloids are 3D structures generated from pluripotent stem cells recapitulating fundamental principles of embryonic pattern formation. Using single-cell genomic analysis, we provide a resource mapping cell states and types during gastruloid development compare them with the in vivo embryo. We developed high-throughput handling imaging pipeline to spatially monitor symmetry breaking report an early spatial variability pluripotency determining binary response Wnt activation. Although gastruloid-core revert pluripotency, peripheral become primitive streak-like. These two populations subsequently break radial initiate axial elongation. By performing compound screen, perturbing thousands gastruloids, derive phenotypic landscape infer networks genetic interactions. Finally, using dual modulation, improve formation anterior existing model. This work provides understand how gastruloids develop generate complex patterns vitro.

Язык: Английский

---

Clonally heritable gene expression imparts a layer of diversity within cell types

Cell Systems, Год журнала: 2024, Номер 15(2), С. 149 - 165.e10

Опубликована: Фев. 1, 2024

Cell types can be classified according to shared patterns of transcription. Non-genetic variability among individual cells the same type has been ascribed stochastic transcriptional bursting and transient cell states. Using high-coverage single-cell RNA profiling, we asked whether long-term, heritable differences in gene expression impart diversity within type. Studying clonal human lymphocytes mouse brain cells, uncovered a vast different clones vivo. We combined chromatin accessibility profiling on lymphocyte reveal thousands regulatory regions exhibiting interclonal variation, which could directly linked variation expression. Our findings identify source cellular diversity, may have important implications for how populations are shaped by selective processes development, aging, disease. A record this paper's transparent peer review process is included supplemental information.

Язык: Английский

---

Time-integrated BMP signaling determines fate in a stem cell model for early human development

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Фев. 17, 2024

Abstract How paracrine signals are interpreted to yield multiple cell fate decisions in a dynamic context during human development vivo and vitro remains poorly understood. Here we report an automated tracking method follow signaling histories linked large numbers of pluripotent stem cells (hPSCs). Using unbiased statistical approach, discover that measured BMP history correlates strongly with individual cells. We find response hPSCs varies more the duration than level. However, both level activity control choices only by changing time integral. Therefore, interchangeable this context. In model for patterning embryo, show predict pattern integral correctly predicts changes domains when is perturbed. Our data suggest mechanistically, integrated SOX2.

Язык: Английский

---

Integrating single-cell multi-omics and prior biological knowledge for a functional characterization of the immune system

Nature Immunology, Год журнала: 2024, Номер 25(3), С. 405 - 417

Опубликована: Фев. 27, 2024

Язык: Английский

---

Bridging live-cell imaging and next-generation cancer treatment

Nature reviews. Cancer, Год журнала: 2023, Номер 23(11), С. 731 - 745

Опубликована: Сен. 13, 2023

Язык: Английский

---

Future medicine: from molecular pathways to the collective intelligence of the body

Trends in Molecular Medicine, Год журнала: 2023, Номер 29(9), С. 687 - 710

Опубликована: Июль 20, 2023

The remarkable anatomical homeostasis exhibited by complex living organisms suggests that they are inherently reprogrammable information-processing systems offer numerous interfaces to their physiological and problem-solving capacities. We briefly review data suggesting the multiscale competency of forms affords a new path for biomedicine exploits innate collective intelligence tissues organs. concept tissue-level allostatic goal-directedness is already bearing fruit in clinical practice. sketch roadmap towards 'somatic psychiatry' using advances bioelectricity behavioral neuroscience design methods induce self-repair structure function. Relaxing assumption cellular control mechanisms static, exploiting powerful concepts from cybernetics, science, developmental biology may spark definitive solutions current biomedical challenges.

Язык: Английский

---

Cellular signaling pathways as plastic, proto-cognitive systems: Implications for biomedicine

Patterns, Год журнала: 2023, Номер 4(5), С. 100737 - 100737

Опубликована: Апрель 26, 2023

Many aspects of health and disease are modeled using the abstraction a "pathway"—a set protein or other subcellular activities with specified functional linkages between them. This metaphor is paradigmatic case deterministic, mechanistic framework that focuses biomedical intervention strategies on altering members this network up-/down-regulation links them—rewiring molecular hardware. However, pathways transcriptional networks exhibit interesting unexpected capabilities such as trainability (memory) information processing in context-sensitive manner. Specifically, they may be amenable to manipulation via their history stimuli (equivalent experiences behavioral science). If true, would enable new class interventions target dynamic physiological "software" implemented by gene-regulatory networks. Here, we briefly review clinical laboratory data show how high-level cognitive inputs pathway modulation interact determine outcomes vivo. Further, propose an expanded view from perspective basal cognition argue broader understanding process contextual across scales will catalyze progress many areas physiology neurobiology. We fuller functionality tractability must go beyond focus details drug structure encompass well embedding within higher levels organization organism, numerous implications for science addressing disease. Exploiting tools concepts sciences explore proto-cognitive underlying more than philosophical stance biochemical processes; at stake roadmap overcoming limitations today's pharmacological inferring future therapeutic wide range states.

Язык: Английский

---

Making human immune systems more interpretable through systems immunology

Trends in Immunology, Год журнала: 2023, Номер 44(8), С. 577 - 584

Опубликована: Июль 3, 2023

Systems immunology is the study of cell–cell interactions in immune system, their regulatory functions, and emergent properties responses.We posit that, despite large interindividual variation, cell composition nonrandom, understanding its rules will make human systems more predictable future.A growing number computational tools exists for inference relationships, but no 'gold standard' methods exist, statistical power often limiting.Minimizing technical sources variance by optimal experimental design sampling procedures allows biological 'signals' to be discovered. A approach necessary comprehend complexity an organism's system since there underlying shared mechanism relationships. Better inferences are essential increase our responses various health conditions. well-planned longitudinal whole blood vital translating vitro findings vivo biology, allowing systematic tracking over time, facilitating development accurate models with improved predictability behaviors. Imagine standing front famous water lilies painting Monet. Gazing from afar, you admire carefully chosen colors beautiful scenery. However, as move closer, expecting see detail, patterns dissolve into a disorganized collection brush strokes, it becomes difficult distinguish that were so clear distance. Just Monet's paintings composed countless small strokes combine form painting, many individual cells, proteins, molecules represent complex intricate network interacting agents. Now, if aspiring artist, must stand close understand how up spectacular color. But just important take step back, view picture, think yourself 'what does this image represent?', examining all components truly artist's motive reasoning. Like consists multiple elements, different populations specialized functions. Achieving balance these key healthy immune-system function overall individual; indeed, activate inhibit each other, compete growth factors ligands, out compartmentalized organs logic and, while doing so, maintain tune thresholds activation remain tolerant surrounding cells tissues, yet responsive relative changes potentially harmful processes targets [1.Parkin J. Cohen B. An overview system.Lancet. 2001; 357: 1777-1789Abstract Full Text PDF PubMed Scopus (791) Google Scholar, 2.Brodin P. et al.NK education: not on-off switch tunable rheostat.Trends Immunol. 2009; 4: 143-149Abstract (188) 3.Grossman Z. Paul W.E. Dynamic tuning lymphocytes: physiological basis, mechanisms, function.Annu. Rev. 2015; 1: 677-713Crossref (63) Scholar]. The compelling apt subject biology research, distributed, multiagent properties. It adaptive (CAS), self-organized, regulated dynamical capacity respond environmental both collectively individually [4.Mitleton-Kelly E. Complex Evolutionary Perspectives on Organisations: Application Complexity Theory Organisations. Pergamon, 2003Google 5.Holland J.H. Signals Boundaries: Building Blocks Adaptive Systems. MIT Press, 2014Google 6.Ahmed Hashish A. On modelling system.Theory Biosci. 2006; 124: 413-418Crossref (22) Therefore, higher-order functions comprehensive analyses involving simultaneously required. Only then can we fully consequences activating one or several like taking back clearly. In opinion article, introduce concept discuss considered, methodological analytical, successful application strategy. We also present examples clinical impact have, general hypothesis being only holistic provide full disease. fact structured CAS mean lacks order structure among components. There certainly logical mechanisms at play well, although most unknown. From evolutionary perspective, survival environment microbes has depended potent defense have played dominant role shaping [7.Quintana-Murci L. al.Immunology natura: clinical, epidemiological genetics infectious diseases.Nat. 2007; 8: 1165-1171Crossref (144) Recent advances single-cell equipped us perform capturing immune-cell within tissue sample some functional cell, thereby examine relationships scale first time (Figure 1A, Key figure ). When seeing correlated two populations, could either indicate coordinated influence third influencing population 1B). Such possible impossible disentangle without further mechanistic experiments, monitoring blood, when possible, permits causal modeling series data [8.Lakshmikanth T. al.Human variation during 1 year.Cell Rep. 2020; 32107923Abstract (18) Our laboratory's internal illustrate nonrandom reproducible correlation types. For illustration purposes: preliminary work (which remains validated), analyzed 1644 samples individuals using 56-parameter mass cytometry panel; noticed strong correlations between frequencies types circulation 1C) (Forlin al., unpublished). example, inverse neutrophil abundance natural killer (NK) B conversely, positive plasmacytoid dendritic (pDCs) eosinophils monocytes 1C). This finding suggests exist individuals, preventing complete chaos. particularly interesting because unique individual, shaped heritable nonheritable (such upbringing, microbiota, age) [9.Carr E.J. al.The cellular age cohabitation.Nat. 2016; 461-468Crossref 10.Reichert al.Lymphocyte subset reference ranges adult Caucasians.Clin. Immunopathol. 1991; 2: 190-208Crossref (289) 11.Tollerud D.J. age, race, gender peripheral mononuclear-cell subsets nonsmokers.J. Clin. 1989; 3: 214-222Crossref (142) 12.Hill D.L. al.Immune varies according location, anemia African children.Sci. Transl. Med. 12eaaw9522Crossref (40) 13.Schluter gut microbiota associated dynamics humans.Nature. 588: 303-307Crossref (184) Consequently, considerable amount variability immunological profiles across exists. Many characteristics – such frequencies, cytokine responses, serum proteins impacted influences cytomegalovirus seropositivity [14.The Milieu Intérieur Consortium al.Natural parameters innate preferentially driven genetic factors.Nat. 2018; 302-314Google Scholar,15.Brodin al.Variation largely non-heritable influences.Cell. 1–2: 37-47Abstract (641) Some become variable NK T (Treg) well interleukin (IL)-15 IL-17 protein concentrations suggesting cumulative exposures [15.Brodin Other display influence, matching phenotype KIR/LIR (killer inhibitory receptor/leukocyte Ig-like receptor) major histocompatibility class I alleles CD39 expression Tregs, CD32 myeloid [16.Mangino M. al.Innate traits differentially affected Commun. 2017; 13850Crossref (77) Scholar,17.Roederer architecture system: bioresource autoimmunity disease pathogenesis.Cell. 387-403Abstract (194) While Scholar,18.Tsang J.S. al.Global reveal baseline predictors postvaccination responses.Cell. 2014; 499-513Abstract (295) Scholar], mostly stable time-scale months, absence infections other perturbations Scholar,19.Brodin Davis M.M. Human variation.Nat. 21-29Crossref (344) One goals contribute advancement personalized medicine, vaccine development, therapies. better pathology immune-related diseases, cancer, autoimmune diseases [20.Germain R.N. Schwartzberg P.L. condition: perspective.Nat. 2011; 5: 369-372Crossref (16) Scholar,21.Germain Will deliver promise new vaccines?: what really constitutes "systems biology" might facilitate design.Cold Spring Harb. Perspect. Biol. 10a033308Crossref (11) Numerous been made towards goal recent years. [22.Kaczorowski K.J. al.Continuous immunotypes describe predict diverse responses.Proc. Natl. Acad. Sci. U. S. 114: E6097-E6106Crossref (71) Scholar] showed preparations mononuclear (PBMCs), three latent vectors describing predictive measured phosphorylation signal transducer activator transcription (STAT)1, STAT3, STAT5 variety cytokines IL-2, IL-6, IL-7, IL-10, IL-21, interferon (IFN)-α, IFN-γ exogenously added PBMCs vitro. Extensive research dedicated defining state antibody following vaccination, significant progress blood-cell longitudinally populations— after influenza virus vaccination [measured adjusted maximum fold change (adjMFC) depend pre-existing concentrations] [18.Tsang Scholar,23.Nakaya H.I. al.Systems analysis immunity years reveals molecular signatures.Immunity. 6: 1186-1198Abstract (196) Scholar,24.Kotliarov Y. al.Broad underlies set point signatures responsiveness activity patients lupus.Nat. 618-629Crossref (80) implications systems' states uncovered future possibly responses. [25.Fourati al.Pan-vaccine endotypes vaccination.Nat. 2022; 12: 1777-1787Crossref (7) distinct transcriptional observed adults prior models, where enriched nuclear factor κB (NF-κB) pathway elevated month vaccination. prevaccination signature was common response 13 vaccines, including virus, malaria, yellow fever smallpox, pneumococcus, hepatitis vaccinations. These results indicated nonclassical likely compared (sc) mRNA-sequencing datasets Recently, [26.Mulè M.P. al.Multiscale integration variations unadjuvanted high responders naturally adjuvanted.medRxiv. 2023; (Published online March 20, 2023. https://doi.org/10.1101/2023.03.20.23287474)PubMed vaccine-induced varied low responders. included tissues; thus, again found drivers kinetics responders, classical mucosal invariant (MAIT) cells. context vaccinations, group [24.Kotliarov identified transcriptome ten genes (including C15orf57, LONP2, PAPSS2, EPHB1, ADAM12, SMC1A, RETN, ENPP1, CD101, C2orf63) temporally frequency CD19+CD20+CD38++B which adjMFC implied less readily vaccine, irrespective specificity proposed serve indicator system's 'set point' higher vaccinations thus enabling identification before based prevaccine states. same magnitude plasmablast-associated flares cohort consisting systemic lupus erythematosus, evaluated times activity. suggested gene should isolated instances, rather similar inflammatory activities enable range Even though vary certain seem all. transcriptomic, antibody, cytokine, cell-population-frequency individuals. help behavior lead valid conclusions concerning whole, ultimate quests immunology. unidentified. highly interactive continuously active communication pathways, vaccines diseases. increased availability advancements transcriptomic led increasing interest inferencing communications. Indeed, highlighting pathways/interactions [27.Jin al.Inference CellChat.Nat. 2021; 1088Crossref (756) 28.Efremova al.CellPhoneDB: inferring combined multi-subunit ligand–receptor complexes.Nat. Protoc. 1484-1506Crossref (937) 29.Browaeys R. al.NicheNet: intercellular linking ligands target genes.Nat. Methods. 159-162Crossref (410) 30.Müller C. al.Removing batch effects - quantile normalization plus combat best microarray data.PLoS ONE. 11e0156594Crossref (82) 31.Stuart al.Comprehensive data.Cell. 2019; 177: 1888-1902.e21Abstract (5042) making interpretations scRNA sequencing available. creating hypotheses why level. Common they rely knowledge calculate likelihood ligand (source subset) receptor (target subset). basis used compute interaction scores differ strategies gold standard currently robust noise, choice method resource [32.Dimitrov D. al.Comparison resources RNA-Seq data.Nat. 3224Crossref (27) now, need interpreted caution and/or validated further, generate valuable regarding observations. Future reliable would great value Informational exchange establishes circuit [33.Hart al.Design principles circuits paradoxical components.Proc. 2012; 109: 8346-8351Crossref (56) Scholar,34.Zhou X. al.Circuit features two-cell system.Cell. 744-757.e17Abstract (176) even basic potential topologies. explored [34.Zhou model created simulate macrophages fibroblasts, reached stability respect macrophage–fibroblast ratio. ratio resilient perturbations, colony-stimulating (CSF1), platelet-derived (PDGFB), additional macrophages, below carrying (as case biology). As such, authors able exchanges information elegant controlled Others developed method: scalable arrayed multivalent extracellular screen (SAVEXIS) protein-binding recombinant domains [35.Shilts al.A physical wiring diagram system.Nature. 608: 397-404Crossref (17) They approximately 57% binding pairs unique, meaning neither had any partner. exclusivity phenomenon prevalent generally recognized signaling roles, CSF1 receptor, BST2-LILRA4 (bone marrow stromal antigen 2–leukocyte immunoglobulin-like subfamily member 4) binding, largest interconnected groups (sharing partners) contained integrins adhesion molecules. this, investigators built simplistic, infer physically interacted. enough consistent published empirical ex leukocytes [36.Vladimer G.I. survey immunomodulatory drugs.Nat. Chem. 13: 681-690Crossref predictions leukocytes. changed strength interactions. Higher-affinity predominated inflamed state, transient dominated resting (possibly supporting dynamic sensing threats) Results publication [37.Kramer B.A. al.Multimodal perception links decision-making single cells.Science. 377: 642-648Crossref (8) suggest influenced input signals about surroundings factors) (i.e., physicochemical state) least interact. Thus, consider condition node (subset cells). Given receiving factors), response/outputs therefore give nonredundant whether state. tempting imagine Scholar,35.Shilts Scholar,37.Kramer measurements occur downstream outputs follow Thereby, agents involved formed. Although much discovered area, current investigation quantitative achieving true systems-level aspect aforementioned approaches accuracy model's translation relies model. evaluate quality inform ensure appropriate intended output. crucial power, too numbers far exceed collected. minimize maximize chances given limitations. developments shown preparation source comparing samples, stimulation-induced fluorescent bead assays [38.Brodin call immunology.Immunity. 1335-1336Abstract (25) PBMC removal neutrophils, effector Also, platelets plasma lost mediate stimulation may than cultures 39.Duffy al.Standardized improves immunomonitoring induced multi-center study.Clin. 183: 325-335Crossref (45) 40.Appay V. al.Immuno-monitoring CD8+ versus samples.J. 309: 192-199Crossref All all, outside organism test tubes culture dishes representative provides depiction environment. Similarly, ideally tissue-specific contexts residing specific tissues [41.Weisberg S.P. al.Tissue-specific changing world.Cell. 1517-1529Abstract (28) To overcome limitation analyses, organoids lymphoid-cell organoids) holds investigations directly studies [42.Wagar L.E. al.Modeling tonsil organoids.Nat. 125-135Crossref Moreover, living organoid capture measurement noise fluctuations interest, stimuli. Examples include circadian rhythms menstrual cycle differences reproductive females function; however, rarely appreciable timepoint measurements. Longitudinal enables dependencies. consideration size accurately reflected minimal noise. use standardized protocols processing, striving run samples/cells together reduce performed. batch, ensuring comparative equally represented batch. reagents cocktails staining prepared once experiment; known minimized. Importantly, plan already defined stage, collection, optimally minimized maximal sensitivity, sufficient maximized opportunities conclusions. mistake collect try solve analytical challenges obtained, leading insignificant difficulties drawing datasets. summary, hope provided convincing evidence advantages studying proposing suitable inferences, whole-blood sampling. highlighted few outlined next steps interpretable through immunology, focusing dynamics. implementing daunting task (see Outstanding questions), believe mysteries finally solved. administration, conditions, more.Outstanding questionsWhat type combination informative dependency regulation?What interactions, required?How generalizable inferred ages, sexes, ancestries? What regulation? required? How Funding Knut och Alice Wallenbergs Stiftelse Award Number 2019.0181 P.B.; Vetenskapsrådet Numbers 2022-01567, 2021-06529, 2020-06190, 2020-02889, 2018-06228, 2019-01495, 2018-06228 Svenska Sällskapet för Medicinsk Forskning CG-22-0148-H-02 P.B. founder Cytodelics AB (Stockholm, Sweden), executive board Kancera scientific advisor Pixelgen Technologies Scailyte AG (Basel, Switzerland) Oxford Immune Algorithmics Inc. (Oxford, UK) Infinant Health (Davis, CA, USA).

Язык: Английский

---

Optogenetic control of Wnt signaling models cell-intrinsic embryogenic patterning using 2D human pluripotent stem cell culture

Development, Год журнала: 2023, Номер 150(14)

Опубликована: Июль 4, 2023

ABSTRACT In embryonic stem cell (ESC) models for early development, spatially and temporally varying patterns of signaling types emerge spontaneously. However, mechanistic insight into this dynamic self-organization is limited by a lack methods spatiotemporal control signaling, the relevance signal dynamics cell-to-cell variability to pattern emergence remains unknown. Here, we combine optogenetic stimulation, imaging transcriptomic approaches study human ESCs (hESC) in two-dimensional (2D) culture. Morphogen were controlled via activation canonical Wnt/β-catenin (optoWnt), which drove broad transcriptional changes mesendoderm differentiation at high efficiency (>99% cells). When activated within subpopulations, optoWnt induced distinct epithelial mesenchymal domains, mediated migration, an mesenchymal-like transition TGFβ signaling. Furthermore, demonstrate that such subpopulations can be used uncover feedback mechanisms between neighboring types. These findings reveal Wnt sufficient generate tissue-scale patterning establish hESC model system investigating relevant embryogenesis.

Язык: Английский

---