1
|
Chen Y, Luan P, Liu J, Wei Y, Wang C, Wu R, Wu Z, Jing M. Spatiotemporally selective astrocytic ATP dynamics encode injury information sensed by microglia following brain injury in mice. Nat Neurosci 2024; 27:1522-1533. [PMID: 38862791 DOI: 10.1038/s41593-024-01680-w] [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: 05/10/2023] [Accepted: 05/13/2024] [Indexed: 06/13/2024]
Abstract
Injuries to the brain result in tunable cell responses paired with stimulus properties, suggesting the existence of intrinsic processes that encode and transmit injury information; however, the molecular mechanism of injury information encoding is unclear. Here, using ATP fluorescent indicators, we identify injury-evoked spatiotemporally selective ATP dynamics, Inflares, in adult mice of both sexes. Inflares are actively released from astrocytes and act as the internal representations of injury. Inflares encode injury intensity and position at their population level through frequency changes and are further decoded by microglia, driving changes in their activation state. Mismatches between Inflares and injury severity lead to microglia dysfunction and worsening of injury outcome. Blocking Inflares in ischemic stroke in mice reduces secondary damage and improves recovery of function. Our results suggest that astrocytic ATP dynamics encode injury information and are sensed by microglia.
Collapse
Affiliation(s)
- Yue Chen
- Chinese Institute for Brain Research, Beijing, China
| | - Pengwei Luan
- Chinese Institute for Brain Research, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Juan Liu
- Chinese Institute for Brain Research, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Yelan Wei
- Chinese Institute for Brain Research, Beijing, China
- Department of College of Physical Education and Sport, Beijing Normal University, Beijing, China
| | - Chenyu Wang
- Chinese Institute for Brain Research, Beijing, China
- Capital Medical University, Basic Medical Sciences, Beijing, China
| | - Rui Wu
- Chinese Institute for Brain Research, Beijing, China
- China Agricultural University, Beijing, China
| | - Zhaofa Wu
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Miao Jing
- Chinese Institute for Brain Research, Beijing, China.
| |
Collapse
|
2
|
Mahajan A, Zaidi ZS, Shukla A, Saxena R, Katti DS. Functionally graded hydrogels with opposing biochemical cues for osteochondral tissue engineering. Biofabrication 2024; 16:035020. [PMID: 38697073 DOI: 10.1088/1758-5090/ad467e] [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: 12/13/2023] [Accepted: 05/02/2024] [Indexed: 05/04/2024]
Abstract
Osteochondral tissue (OC) repair remains a significant challenge in the field of musculoskeletal tissue engineering. OC tissue displays a gradient structure characterized by variations in both cell types and extracellular matrix components, from cartilage to the subchondral bone. These functional gradients observed in the native tissue have been replicated to engineer OC tissuein vitro. While diverse fabrication methods have been employed to create these microenvironments, emulating the natural gradients and effective regeneration of the tissue continues to present a significant challenge. In this study, we present the design and development of CMC-silk interpenetrating (IPN) hydrogel with opposing dual biochemical gradients similar to native tissue with the aim to regenerate the complete OC unit. The gradients of biochemical cues were generated using an in-house-built extrusion system. Firstly, we fabricated a hydrogel that exhibits a smooth transition of sulfated carboxymethyl cellulose (sCMC) and TGF-β1 (SCT gradient hydrogel) from the upper to the lower region of the IPN hydrogel to regenerate the cartilage layer. Secondly, a hydrogel with a hydroxyapatite (HAp) gradient (HAp gradient hydrogel) from the lower to the upper region was fabricated to facilitate the regeneration of the subchondral bone layer. Subsequently, we developed a dual biochemical gradient hydrogel with a smooth transition of sCMC + TGF-β1 and HAp gradients in opposing directions, along with a blend of both biochemical cues in the middle. The results showed that the dual biochemical gradient hydrogels with biochemical cues corresponding to the three zones (i.e. cartilage, interface and bone) of the OC tissue led to differentiation of bone-marrow-derived mesenchymal stem cells to zone-specific lineages, thereby demonstrating their efficacy in directing the fate of progenitor cells. In summary, our study provided a simple and innovative method for incorporating gradients of biochemical cues into hydrogels. The gradients of biochemical cues spatially guided the differentiation of stem cells and facilitated tissue growth, which would eventually lead to the regeneration of the entire OC tissue with a smooth transition from cartilage (soft) to bone (hard) tissues. This promising approach is translatable and has the potential to generate numerous biochemical and biophysical gradients for regeneration of other interface tissues, such as tendon-to-muscle and ligament-to-bone.
Collapse
Affiliation(s)
- Aman Mahajan
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology-Kanpur, Kanpur 208016, Uttar Pradesh, India
- The Mehta Family Centre for Engineering in Medicine, Indian Institute of Technology-Kanpur, Kanpur 208016, Uttar Pradesh, India
| | - Zahra Sifat Zaidi
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology-Kanpur, Kanpur 208016, Uttar Pradesh, India
- The Mehta Family Centre for Engineering in Medicine, Indian Institute of Technology-Kanpur, Kanpur 208016, Uttar Pradesh, India
| | - Amit Shukla
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology-Kanpur, Kanpur 208016, Uttar Pradesh, India
| | - Rakshita Saxena
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology-Kanpur, Kanpur 208016, Uttar Pradesh, India
- The Mehta Family Centre for Engineering in Medicine, Indian Institute of Technology-Kanpur, Kanpur 208016, Uttar Pradesh, India
| | - Dhirendra S Katti
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology-Kanpur, Kanpur 208016, Uttar Pradesh, India
- The Mehta Family Centre for Engineering in Medicine, Indian Institute of Technology-Kanpur, Kanpur 208016, Uttar Pradesh, India
| |
Collapse
|
3
|
Shroff NP, Xu P, Kim S, Shelton ER, Gross BJ, Liu Y, Gomez CO, Ye Q, Drennon TY, Hu JK, Green JBA, Campàs O, Klein OD. Proliferation-driven mechanical compression induces signalling centre formation during mammalian organ development. Nat Cell Biol 2024; 26:519-529. [PMID: 38570617 DOI: 10.1038/s41556-024-01380-4] [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: 01/11/2023] [Accepted: 02/15/2024] [Indexed: 04/05/2024]
Abstract
Localized sources of morphogens, called signalling centres, play a fundamental role in coordinating tissue growth and cell fate specification during organogenesis. However, how these signalling centres are established in tissues during embryonic development is still unclear. Here we show that the main signalling centre orchestrating development of rodent incisors, the enamel knot (EK), is specified by a cell proliferation-driven buildup in compressive stresses (mechanical pressure) in the tissue. Direct mechanical measurements indicate that the stresses generated by cell proliferation are resisted by the surrounding tissue, creating a circular pattern of mechanical anisotropy with a region of high compressive stress at its centre that becomes the EK. Pharmacological inhibition of proliferation reduces stresses and suppresses EK formation, and application of external pressure in proliferation-inhibited conditions rescues the formation of the EK. Mechanical information is relayed intracellularly through YAP protein localization, which is cytoplasmic in the region of compressive stress that establishes the EK and nuclear in the stretched anisotropic cells that resist the pressure buildup around the EK. Together, our data identify a new role for proliferation-driven mechanical compression in the specification of a model signalling centre during mammalian organ development.
Collapse
Affiliation(s)
- Neha Pincha Shroff
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, CA, USA
| | - Pengfei Xu
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, CA, USA
| | - Sangwoo Kim
- Department of Mechanical Engineering, University of California, Santa Barbara, CA, USA
- Institute of Mechanical Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Elijah R Shelton
- Department of Mechanical Engineering, University of California, Santa Barbara, CA, USA
| | - Ben J Gross
- Department of Mechanical Engineering, University of California, Santa Barbara, CA, USA
| | - Yucen Liu
- Department of Mechanical Engineering, University of California, Santa Barbara, CA, USA
| | - Carlos O Gomez
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Qianlin Ye
- School of Dentistry, University of California Los Angeles, Los Angeles, CA, USA
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA
| | - Tingsheng Yu Drennon
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, CA, USA
| | - Jimmy K Hu
- School of Dentistry, University of California Los Angeles, Los Angeles, CA, USA
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA
| | - Jeremy B A Green
- Centre for Craniofacial Regeneration and Biology, King's College London, London, UK
| | - Otger Campàs
- Department of Mechanical Engineering, University of California, Santa Barbara, CA, USA.
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA.
- Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany.
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
- Center for Systems Biology Dresden, Dresden, Germany.
| | - Ophir D Klein
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, CA, USA.
- Department of Pediatrics, Cedars-Sinai Guerin Children's, Los Angeles, CA, USA.
| |
Collapse
|
4
|
Wessels HH, Stirn A, Méndez-Mancilla A, Kim EJ, Hart SK, Knowles DA, Sanjana NE. Prediction of on-target and off-target activity of CRISPR-Cas13d guide RNAs using deep learning. Nat Biotechnol 2024; 42:628-637. [PMID: 37400521 DOI: 10.1038/s41587-023-01830-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 05/16/2023] [Indexed: 07/05/2023]
Abstract
Transcriptome engineering applications in living cells with RNA-targeting CRISPR effectors depend on accurate prediction of on-target activity and off-target avoidance. Here we design and test ~200,000 RfxCas13d guide RNAs targeting essential genes in human cells with systematically designed mismatches and insertions and deletions (indels). We find that mismatches and indels have a position- and context-dependent impact on Cas13d activity, and mismatches that result in G-U wobble pairings are better tolerated than other single-base mismatches. Using this large-scale dataset, we train a convolutional neural network that we term targeted inhibition of gene expression via gRNA design (TIGER) to predict efficacy from guide sequence and context. TIGER outperforms the existing models at predicting on-target and off-target activity on our dataset and published datasets. We show that TIGER scoring combined with specific mismatches yields the first general framework to modulate transcript expression, enabling the use of RNA-targeting CRISPRs to precisely control gene dosage.
Collapse
Affiliation(s)
- Hans-Hermann Wessels
- New York Genome Center, New York City, NY, USA
- Department of Biology, New York University, New York City, NY, USA
| | - Andrew Stirn
- New York Genome Center, New York City, NY, USA
- Department of Computer Science, Columbia University, New York City, NY, USA
| | - Alejandro Méndez-Mancilla
- New York Genome Center, New York City, NY, USA
- Department of Biology, New York University, New York City, NY, USA
| | - Eric J Kim
- Department of Computer Science, Columbia University, New York City, NY, USA
| | - Sydney K Hart
- New York Genome Center, New York City, NY, USA
- Department of Biology, New York University, New York City, NY, USA
| | - David A Knowles
- New York Genome Center, New York City, NY, USA.
- Department of Computer Science, Columbia University, New York City, NY, USA.
- Data Science Institute, Columbia University, New York City, NY, USA.
- Department of Systems Biology, Columbia University, New York City, NY, USA.
| | - Neville E Sanjana
- New York Genome Center, New York City, NY, USA.
- Department of Biology, New York University, New York City, NY, USA.
| |
Collapse
|
5
|
Bhat GR, Sethi I, Sadida HQ, Rah B, Mir R, Algehainy N, Albalawi IA, Masoodi T, Subbaraj GK, Jamal F, Singh M, Kumar R, Macha MA, Uddin S, Akil ASAS, Haris M, Bhat AA. Cancer cell plasticity: from cellular, molecular, and genetic mechanisms to tumor heterogeneity and drug resistance. Cancer Metastasis Rev 2024; 43:197-228. [PMID: 38329598 PMCID: PMC11016008 DOI: 10.1007/s10555-024-10172-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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 01/24/2024] [Indexed: 02/09/2024]
Abstract
Cancer is a complex disease displaying a variety of cell states and phenotypes. This diversity, known as cancer cell plasticity, confers cancer cells the ability to change in response to their environment, leading to increased tumor diversity and drug resistance. This review explores the intricate landscape of cancer cell plasticity, offering a deep dive into the cellular, molecular, and genetic mechanisms that underlie this phenomenon. Cancer cell plasticity is intertwined with processes such as epithelial-mesenchymal transition and the acquisition of stem cell-like features. These processes are pivotal in the development and progression of tumors, contributing to the multifaceted nature of cancer and the challenges associated with its treatment. Despite significant advancements in targeted therapies, cancer cell adaptability and subsequent therapy-induced resistance remain persistent obstacles in achieving consistent, successful cancer treatment outcomes. Our review delves into the array of mechanisms cancer cells exploit to maintain plasticity, including epigenetic modifications, alterations in signaling pathways, and environmental interactions. We discuss strategies to counteract cancer cell plasticity, such as targeting specific cellular pathways and employing combination therapies. These strategies promise to enhance the efficacy of cancer treatments and mitigate therapy resistance. In conclusion, this review offers a holistic, detailed exploration of cancer cell plasticity, aiming to bolster the understanding and approach toward tackling the challenges posed by tumor heterogeneity and drug resistance. As articulated in this review, the delineation of cellular, molecular, and genetic mechanisms underlying tumor heterogeneity and drug resistance seeks to contribute substantially to the progress in cancer therapeutics and the advancement of precision medicine, ultimately enhancing the prospects for effective cancer treatment and patient outcomes.
Collapse
Affiliation(s)
- Gh Rasool Bhat
- Advanced Centre for Human Genetics, Sher-I-Kashmir Institute of Medical Sciences, Soura, Srinagar, Jammu and Kashmir, India
| | - Itty Sethi
- Institute of Human Genetics, University of Jammu, Jammu, Jammu and Kashmir, India
| | - Hana Q Sadida
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity and Cancer Program, Sidra Medicine, Doha, Qatar
| | - Bilal Rah
- Iron Biology Group, Research Institute of Medical and Health Science, University of Sharjah, Sharjah, UAE
| | - Rashid Mir
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, Prince Fahad Bin Sultan Chair for Biomedical Research, University of Tabuk, Tabuk, Saudi Arabia
| | - Naseh Algehainy
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, Prince Fahad Bin Sultan Chair for Biomedical Research, University of Tabuk, Tabuk, Saudi Arabia
| | | | - Tariq Masoodi
- Laboratory of Cancer Immunology and Genetics, Sidra Medicine, Doha, Qatar
| | | | - Farrukh Jamal
- Dr. Rammanohar, Lohia Avadh University, Ayodhya, India
| | - Mayank Singh
- Department of Medical Oncology (Lab.), Institute of Medical Sciences (AIIMS), Dr. BRAIRCH, All India, New Delhi, India
| | - Rakesh Kumar
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
| | - Muzafar A Macha
- Watson-Crick Centre for Molecular Medicine, Islamic University of Science and Technology, Awantipora, Jammu and Kashmir, India
| | - Shahab Uddin
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
- Laboratory Animal Research Centre, Qatar University, Doha, Qatar
| | - Ammira S Al-Shabeeb Akil
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity and Cancer Program, Sidra Medicine, Doha, Qatar
| | - Mohammad Haris
- Laboratory Animal Research Centre, Qatar University, Doha, Qatar.
- Center for Advanced Metabolic Imaging in Precision Medicine, Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA.
| | - Ajaz A Bhat
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity and Cancer Program, Sidra Medicine, Doha, Qatar.
| |
Collapse
|
6
|
Akiyama T, Raftery LA, Wharton KA. Bone morphogenetic protein signaling: the pathway and its regulation. Genetics 2024; 226:iyad200. [PMID: 38124338 PMCID: PMC10847725 DOI: 10.1093/genetics/iyad200] [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: 07/31/2023] [Accepted: 10/27/2023] [Indexed: 12/23/2023] Open
Abstract
In the mid-1960s, bone morphogenetic proteins (BMPs) were first identified in the extracts of bone to have the remarkable ability to induce heterotopic bone. When the Drosophila gene decapentaplegic (dpp) was first identified to share sequence similarity with mammalian BMP2/BMP4 in the late-1980s, it became clear that secreted BMP ligands can mediate processes other than bone formation. Following this discovery, collaborative efforts between Drosophila geneticists and mammalian biochemists made use of the strengths of their respective model systems to identify BMP signaling components and delineate the pathway. The ability to conduct genetic modifier screens in Drosophila with relative ease was critical in identifying the intracellular signal transducers for BMP signaling and the related transforming growth factor-beta/activin signaling pathway. Such screens also revealed a host of genes that encode other core signaling components and regulators of the pathway. In this review, we provide a historical account of this exciting time of gene discovery and discuss how the field has advanced over the past 30 years. We have learned that while the core BMP pathway is quite simple, composed of 3 components (ligand, receptor, and signal transducer), behind the versatility of this pathway lies multiple layers of regulation that ensures precise tissue-specific signaling output. We provide a sampling of these discoveries and highlight many questions that remain to be answered to fully understand the complexity of BMP signaling.
Collapse
Affiliation(s)
- Takuya Akiyama
- Department of Biology, Rich and Robin Porter Cancer Research Center, The Center for Genomic Advocacy, Indiana State University, Terre Haute, IN 47809, USA
| | - Laurel A Raftery
- School of Life Sciences, University of Nevada, 4505 S. Maryland Parkway, Las Vegas, NV 89154, USA
| | - Kristi A Wharton
- Department of Molecular Biology, Cell Biology, and Biochemistry, Carney Institute for Brain Science, Brown University, Providence, RI 02912, USA
| |
Collapse
|
7
|
Tsutsumi-Arai C, Arai Y, Tran A, Salinas M, Nakai Y, Orikasa S, Ono W, Ono N. A PTHrP Gradient Drives Mandibular Condylar Chondrogenesis via Runx2. J Dent Res 2024; 103:91-100. [PMID: 38058151 PMCID: PMC10734211 DOI: 10.1177/00220345231208175] [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: 12/08/2023] Open
Abstract
The mandibular condylar cartilage (MCC) is an essential component of the temporomandibular joint, which orchestrates the vertical growth of the mandibular ramus through endochondral ossification with distinctive modes of cell differentiation. Parathyroid hormone-related protein (PTHrP) is a master regulator of chondrogenesis; in the long bone epiphyseal growth plate, PTHrP expressed by resting zone chondrocytes promotes chondrocyte proliferation in the adjacent layer. However, how PTHrP regulates chondrogenesis in the MCC remains largely unclear. In this study, we used a Pthrp-mCherry knock-in reporter strain to map the localization of PTHrP+ cells in the MCC and define the function of PTHrP in the growing mandibular condyle. In the postnatal MCC of PthrpmCherry/+ mice, PTHrP-mCherry was specifically expressed by cells in the superficial layer immediately adjacent to RUNX2-expressing cells in the polymorphic layer. PTHrP ligands diffused across the polymorphic and chondrocyte layers where its cognate receptor PTH1R was abundantly expressed. We further analyzed the mandibular condyle of PthrpmCherry/mCherry mice lacking functional PTHrP protein (PTHrP-KO). At embryonic day (E) 18.5, the condylar process and MCC were significantly truncated in the PTHrP-KO mandible, which was associated with a significant reduction in cell proliferation across the polymorphic layer and a loss of SOX9+ cells in the chondrocyte layers. The PTHrP-KO MCC showed a transient increase in the number of Col10a1+ hypertrophic chondrocytes at E15.5, followed by a significant loss of these cells at E18.5, indicating that superficial layer-derived PTHrP prevents premature chondrocyte exhaustion in the MCC. The expression of Runx2, but not Sp7, was significantly reduced in the polymorphic layer of the PTHrP-KO MCC. Therefore, PTHrP released from cells in the superficial layer directly acts on cells in the polymorphic layer to promote proliferation of chondrocyte precursor cells and prevent their premature differentiation by maintaining Runx2 expression, revealing a unique PTHrP gradient-directed mechanism that regulates MCC chondrogenesis.
Collapse
Affiliation(s)
- C. Tsutsumi-Arai
- University of Texas Health Science Center at Houston School of Dentistry, Houston, TX, USA
| | - Y. Arai
- University of Texas Health Science Center at Houston School of Dentistry, Houston, TX, USA
| | - A. Tran
- University of Texas Health Science Center at Houston School of Dentistry, Houston, TX, USA
| | - M. Salinas
- University of Texas Health Science Center at Houston School of Dentistry, Houston, TX, USA
| | - Y. Nakai
- University of Texas Health Science Center at Houston School of Dentistry, Houston, TX, USA
| | - S. Orikasa
- University of Texas Health Science Center at Houston School of Dentistry, Houston, TX, USA
| | - W. Ono
- University of Texas Health Science Center at Houston School of Dentistry, Houston, TX, USA
| | - N. Ono
- University of Texas Health Science Center at Houston School of Dentistry, Houston, TX, USA
| |
Collapse
|
8
|
Ishitani T. Cadherin-linked morphogen gradient actualizes robust tissue patterning. Curr Opin Cell Biol 2023; 85:102275. [PMID: 37944424 DOI: 10.1016/j.ceb.2023.102275] [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: 09/02/2023] [Revised: 09/30/2023] [Accepted: 10/14/2023] [Indexed: 11/12/2023]
Abstract
Morphogen gradients govern tissue patterning. These gradients provide positional information, instructing cells to adopt distinct fates. Over the past few decades, extensive studies have revealed the detailed mechanisms by which morphogens generate tissue patterns. However, the communication between morphogen-receiving cells is still poorly understood. Here, I describe how cadherin-mediated cell competition ensures robust morphogen-gradient formation. In normal zebrafish embryos, unfit cells with abnormal Wnt signaling activity spontaneously appear and produce a noisy morphogen gradient. These unfit cells communicate with neighboring cells through cadherins and are subsequently killed by cell competition. This process of killing unfit cells corrects noisy gradients to support reproducible patterning. I also discuss the significance of cell-competition-mediated morphogen-gradient correction from the perspectives of evolution and disease biology.
Collapse
Affiliation(s)
- Tohru Ishitani
- Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan; Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka 565-0871, Japan.
| |
Collapse
|
9
|
Snell-Rood EC, Ehlman SM. Developing the genotype-to-phenotype relationship in evolutionary theory: A primer of developmental features. Evol Dev 2023; 25:393-409. [PMID: 37026670 DOI: 10.1111/ede.12434] [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: 09/28/2022] [Revised: 02/09/2023] [Accepted: 03/16/2023] [Indexed: 04/08/2023]
Abstract
For decades, there have been repeated calls for more integration across evolutionary and developmental biology. However, critiques in the literature and recent funding initiatives suggest this integration remains incomplete. We suggest one way forward is to consider how we elaborate the most basic concept of development, the relationship between genotype and phenotype, in traditional models of evolutionary processes. For some questions, when more complex features of development are accounted for, predictions of evolutionary processes shift. We present a primer on concepts of development to clarify confusion in the literature and fuel new questions and approaches. The basic features of development involve expanding a base model of genotype-to-phenotype to include the genome, space, and time. A layer of complexity is added by incorporating developmental systems, including signal-response systems and networks of interactions. The developmental emergence of function, which captures developmental feedbacks and phenotypic performance, offers further model elaborations that explicitly link fitness with developmental systems. Finally, developmental features such as plasticity and developmental niche construction conceptualize the link between a developing phenotype and the external environment, allowing for a fuller inclusion of ecology in evolutionary models. Incorporating aspects of developmental complexity into evolutionary models also accommodates a more pluralistic focus on the causal importance of developmental systems, individual organisms, or agents in generating evolutionary patterns. Thus, by laying out existing concepts of development, and considering how they are used across different fields, we can gain clarity in existing debates around the extended evolutionary synthesis and pursue new directions in evolutionary developmental biology. Finally, we consider how nesting developmental features in traditional models of evolution can highlight areas of evolutionary biology that need more theoretical attention.
Collapse
Affiliation(s)
- Emilie C Snell-Rood
- Department of Ecology, Evolution and Behavior, University of Minnesota, St Paul, Minnesota, USA
| | - Sean M Ehlman
- Department of Ecology, Evolution and Behavior, University of Minnesota, St Paul, Minnesota, USA
- SCIoI Excellence Cluster, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Humboldt University, Berlin, Germany
| |
Collapse
|
10
|
Walker BL, Nie Q. NeST: nested hierarchical structure identification in spatial transcriptomic data. Nat Commun 2023; 14:6554. [PMID: 37848426 PMCID: PMC10582109 DOI: 10.1038/s41467-023-42343-x] [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: 06/13/2023] [Accepted: 10/06/2023] [Indexed: 10/19/2023] Open
Abstract
Spatial gene expression in tissue is characterized by regions in which particular genes are enriched or depleted. Frequently, these regions contain nested inside them subregions with distinct expression patterns. Segmentation methods in spatial transcriptomic (ST) data extract disjoint regions maximizing similarity over the greatest number of genes, typically on a particular spatial scale, thus lacking the ability to find region-within-region structure. We present NeST, which extracts spatial structure through coexpression hotspots-regions exhibiting localized spatial coexpression of some set of genes. Coexpression hotspots identify structure on any spatial scale, over any possible subset of genes, and are highly explainable. NeST also performs spatial analysis of cell-cell interactions via ligand-receptor, identifying active areas de novo without restriction of cell type or other groupings, in both two and three dimensions. Through application on ST datasets of varying type and resolution, we demonstrate the ability of NeST to reveal a new level of biological structure.
Collapse
Affiliation(s)
- Benjamin L Walker
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California Irvine, Irvine, CA, 92627, USA
- Department of Mathematics, University of California Irvine, Irvine, CA, 92627, USA
| | - Qing Nie
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California Irvine, Irvine, CA, 92627, USA.
- Department of Mathematics, University of California Irvine, Irvine, CA, 92627, USA.
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA, 92627, USA.
| |
Collapse
|
11
|
Chitra U, Arnold BJ, Sarkar H, Ma C, Lopez-Darwin S, Sanno K, Raphael BJ. Mapping the topography of spatial gene expression with interpretable deep learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.10.561757. [PMID: 37873258 PMCID: PMC10592770 DOI: 10.1101/2023.10.10.561757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Spatially resolved transcriptomics technologies provide high-throughput measurements of gene expression in a tissue slice, but the sparsity of this data complicates the analysis of spatial gene expression patterns such as gene expression gradients. We address these issues by deriving a topographic map of a tissue slice-analogous to a map of elevation in a landscape-using a novel quantity called the isodepth. Contours of constant isodepth enclose spatial domains with distinct cell type composition, while gradients of the isodepth indicate spatial directions of maximum change in gene expression. We develop GASTON, an unsupervised and interpretable deep learning algorithm that simultaneously learns the isodepth, spatial gene expression gradients, and piecewise linear functions of the isodepth that model both continuous gradients and discontinuous spatial variation in the expression of individual genes. We validate GASTON by showing that it accurately identifies spatial domains and marker genes across several biological systems. In SRT data from the brain, GASTON reveals gradients of neuronal differentiation and firing, and in SRT data from a tumor sample, GASTON infers gradients of metabolic activity and epithelial-mesenchymal transition (EMT)-related gene expression in the tumor microenvironment.
Collapse
Affiliation(s)
- Uthsav Chitra
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Brian J. Arnold
- Department of Computer Science, Princeton University, Princeton, NJ, USA
- Center for Statistics and Machine Learning, Princeton University, Princeton, NJ, USA
| | - Hirak Sarkar
- Department of Computer Science, Princeton University, Princeton, NJ, USA
- Ludwig Cancer Institute, Princeton Branch, Princeton University, Princeton, NJ, USA
| | - Cong Ma
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | | | - Kohei Sanno
- Department of Computer Science, Princeton University, Princeton, NJ, USA
- Center for Statistics and Machine Learning, Princeton University, Princeton, NJ, USA
| | | |
Collapse
|
12
|
Mim MS, Knight C, Zartman JJ. Quantitative insights in tissue growth and morphogenesis with optogenetics. Phys Biol 2023; 20:061001. [PMID: 37678266 PMCID: PMC10594237 DOI: 10.1088/1478-3975/acf7a1] [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: 01/20/2023] [Revised: 08/15/2023] [Accepted: 09/07/2023] [Indexed: 09/09/2023]
Abstract
Cells communicate with each other to jointly regulate cellular processes during cellular differentiation and tissue morphogenesis. This multiscale coordination arises through the spatiotemporal activity of morphogens to pattern cell signaling and transcriptional factor activity. This coded information controls cell mechanics, proliferation, and differentiation to shape the growth and morphogenesis of organs. While many of the molecular components and physical interactions have been identified in key model developmental systems, there are still many unresolved questions related to the dynamics involved due to challenges in precisely perturbing and quantitatively measuring signaling dynamics. Recently, a broad range of synthetic optogenetic tools have been developed and employed to quantitatively define relationships between signal transduction and downstream cellular responses. These optogenetic tools can control intracellular activities at the single cell or whole tissue scale to direct subsequent biological processes. In this brief review, we highlight a selected set of studies that develop and implement optogenetic tools to unravel quantitative biophysical mechanisms for tissue growth and morphogenesis across a broad range of biological systems through the manipulation of morphogens, signal transduction cascades, and cell mechanics. More generally, we discuss how optogenetic tools have emerged as a powerful platform for probing and controlling multicellular development.
Collapse
Affiliation(s)
- Mayesha Sahir Mim
- Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, United States of America
| | - Caroline Knight
- Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, United States of America
| | - Jeremiah J Zartman
- Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, United States of America
| |
Collapse
|
13
|
Paladino O, Moranda A, Falugi C. Spatiotemporal role of muscarinic signaling in early chick development: exposure to cholinomimetic agents by a mathematical model. Cell Biol Toxicol 2023; 39:1453-1469. [PMID: 36098822 PMCID: PMC10425487 DOI: 10.1007/s10565-022-09770-w] [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: 01/13/2022] [Accepted: 08/26/2022] [Indexed: 11/02/2022]
Abstract
Awareness is growing that, besides several neurotoxic effects, cholinomimetic drugs able to interfere the cholinergic neurotransmitter system may exert a teratogen effect in developing embryos of vertebrate and invertebrate organisms. Cholinomimetic substances exert their toxic activity on organisms as they inhibit the functionality of the cholinergic system by completely or partially replacing the ACh molecule both at the level of the AChE active site and at the level of acetylcholine receptors. In this work, we focused the attention on the effects of muscarinic antagonist (atropine) and agonist (carbachol) drugs during the early development and ontogenesis of chick embryos. An unsteady-state mathematical model of the drug release and fate was developed, to synchronize exposure to a gradient of drug concentrations with the different developmental events. Since concentration measures in time and space cannot be taken without damaging the embryo itself, the diffusion model was the only way to establish at each time-step the exact concentration of drug at the different points of the embryo body (considered two-dimensional up to the 50 h stage). This concentration depends on the distance and position of the embryo with respect to the releasing source. The exposure to carbachol generally enhanced dimensions and stages of the embryos, while atropine mainly caused delay in development and small size of the embryos. Both the drugs were able to cause developmental anomalies, depending on the moment of development, in a time- and dose-dependent way, regardless the expression of genes driving each event. 1. Early chick embryos were exposed to muscarinic drugs in a spatial-temporal context. 2. Effects were stage-(time) dependent, according to distance and position of the source. 3. Atropine inhibited growth, mainly interfering with the cephalic process formation and heart differentiation; carbachol increased growth reducing differentiation. 4. Interferences may be exerted by alteration of calcium responses to naturally occurring morphogen-driven mechanisms.
Collapse
Affiliation(s)
- Ombretta Paladino
- Department of Civil, Chemical and Environmental Engineering (DICCA), University of Genoa, Via Opera Pia 15, 16145 Genoa, Italy
| | - Arianna Moranda
- Department of Civil, Chemical and Environmental Engineering (DICCA), University of Genoa, Via Opera Pia 15, 16145 Genoa, Italy
| | - Carla Falugi
- Department of Earth, Environmental and Life Sciences (DISTAV), University of Genoa, Corso Europa 26, 16132 Genoa, Italy
| |
Collapse
|
14
|
Kyomen S, Murillo-Rincón AP, Kaucká M. Evolutionary mechanisms modulating the mammalian skull development. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220080. [PMID: 37183900 PMCID: PMC10184257 DOI: 10.1098/rstb.2022.0080] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
Mammals possess impressive craniofacial variation that mirrors their adaptation to diverse ecological niches, feeding behaviour, physiology and overall lifestyle. The spectrum of craniofacial geometries is established mainly during embryonic development. The formation of the head represents a sequence of events regulated on genomic, molecular, cellular and tissue level, with each step taking place under tight spatio-temporal control. Even minor variations in timing, position or concentration of the molecular drivers and the resulting events can affect the final shape, size and position of the skeletal elements and the geometry of the head. Our knowledge of craniofacial development increased substantially in the last decades, mainly due to research using conventional vertebrate model organisms. However, how developmental differences in head formation arise specifically within mammals remains largely unexplored. This review highlights three evolutionary mechanisms acknowledged to modify ontogenesis: heterochrony, heterotopy and heterometry. We present recent research that links changes in developmental timing, spatial organization or gene expression levels to the acquisition of species-specific skull morphologies. We highlight how these evolutionary modifications occur on the level of the genes, molecules and cellular processes, and alter conserved developmental programmes to generate a broad spectrum of skull shapes characteristic of the class Mammalia. This article is part of the theme issue 'The mammalian skull: development, structure and function'.
Collapse
Affiliation(s)
- Stella Kyomen
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, Plön 24306, Germany
| | - Andrea P Murillo-Rincón
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, Plön 24306, Germany
| | - Markéta Kaucká
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, Plön 24306, Germany
| |
Collapse
|
15
|
Pierini G, Dahmann C. Hedgehog morphogen gradient is robust towards variations in tissue morphology in Drosophila. Sci Rep 2023; 13:8454. [PMID: 37231029 DOI: 10.1038/s41598-023-34632-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 05/04/2023] [Indexed: 05/27/2023] Open
Abstract
During tissue development, gradients of secreted signaling molecules known as morphogens provide cells with positional information. The mechanisms underlying morphogen spreading have been widely studied, however, it remains largely unexplored whether the shape of morphogen gradients is influenced by tissue morphology. Here, we developed an analysis pipeline to quantify the distribution of proteins within a curved tissue. We applied it to the Hedgehog morphogen gradient in the Drosophila wing and eye-antennal imaginal discs, which are flat and curved tissues, respectively. Despite a different expression profile, the slope of the Hedgehog gradient was comparable between the two tissues. Moreover, inducing ectopic folds in wing imaginal discs did not affect the slope of the Hedgehog gradient. Suppressing curvature in the eye-antennal imaginal disc also did not alter the Hedgehog gradient slope but led to ectopic Hedgehog expression. In conclusion, through the development of an analysis pipeline that allows quantifying protein distribution in curved tissues, we show that the Hedgehog gradient is robust towards variations in tissue morphology.
Collapse
Affiliation(s)
- Giulia Pierini
- School of Science, Technische Universität Dresden, 01062, Dresden, Germany
| | - Christian Dahmann
- School of Science, Technische Universität Dresden, 01062, Dresden, Germany.
- Cluster of Excellence Physics of Life, Technische Universität Dresden, 01062, Dresden, Germany.
| |
Collapse
|
16
|
Zhang Y, Raza A, Xue YQ, Yang G, Hayat U, Yu J, Liu C, Wang HJ, Wang JY. Water-responsive 4D printing based on self-assembly of hydrophobic protein “Zein” for the control of degradation rate and drug release. Bioact Mater 2023; 23:343-352. [DOI: 10.1016/j.bioactmat.2022.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/13/2022] [Accepted: 11/15/2022] [Indexed: 11/27/2022] Open
|
17
|
Hatakeyama Y, Saito N, Mii Y, Takada R, Shinozuka T, Takemoto T, Naoki H, Takada S. Intercellular exchange of Wnt ligands reduces cell population heterogeneity during embryogenesis. Nat Commun 2023; 14:1924. [PMID: 37024462 PMCID: PMC10079677 DOI: 10.1038/s41467-023-37350-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/13/2023] [Indexed: 04/08/2023] Open
Abstract
Wnt signaling is required to maintain bipotent progenitors for neural and paraxial mesoderm cells, the neuromesodermal progenitor (NMP) cells that reside in the epiblast and tailbud. Since epiblast/tailbud cells receive Wnt ligands produced by one another, this exchange may average out the heterogeneity of Wnt signaling levels among these cells. Here, we examined this possibility by replacing endogenous Wnt3a with a receptor-fused form that activates signaling in producing cells, but not in neighboring cells. Mutant mouse embryos show a unique phenotype in which maintenance of many NMP cells is impaired, although some cells persist for long periods. The epiblast cell population of these embryos increases heterogeneity in Wnt signaling levels as embryogenesis progresses and are sensitive to retinoic acid, an endogenous antagonist of NMP maintenance. Thus, mutual intercellular exchange of Wnt ligands in the epiblast cell population reduces heterogeneity and achieves robustness to environmental stress.
Collapse
Affiliation(s)
- Yudai Hatakeyama
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan
- National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan
- The Graduate University for Advanced Studies (SOKENDAI), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan
| | - Nen Saito
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan.
- National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan.
- The Graduate University for Advanced Studies (SOKENDAI), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan.
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8511, Japan.
| | - Yusuke Mii
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan
- National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan
- The Graduate University for Advanced Studies (SOKENDAI), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan
- PREST, Japan Science and Technology Agency (JST), Kawaguchi, Saitama, 332-0012, Japan
| | - Ritsuko Takada
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan
- National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan
| | - Takuma Shinozuka
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan
- National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan
- The Graduate University for Advanced Studies (SOKENDAI), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan
- Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara, 630-0192, Japan
| | - Tatsuya Takemoto
- Institute of Advanced Medical Sciences, Tokushima University, 3-18-5 Kuramoto-cho, Tokushima, Tokushima, 770-8503, Japan
| | - Honda Naoki
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8511, Japan
| | - Shinji Takada
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan.
- National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan.
- The Graduate University for Advanced Studies (SOKENDAI), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan.
| |
Collapse
|
18
|
Pattnaik A, Sanket AS, Pradhan S, Sahoo R, Das S, Pany S, Douglas TEL, Dandela R, Liu Q, Rajadas J, Pati S, De Smedt SC, Braeckmans K, Samal SK. Designing of gradient scaffolds and their applications in tissue regeneration. Biomaterials 2023; 296:122078. [PMID: 36921442 DOI: 10.1016/j.biomaterials.2023.122078] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 02/19/2023] [Accepted: 03/02/2023] [Indexed: 03/07/2023]
Abstract
Gradient scaffolds are isotropic/anisotropic three-dimensional structures with gradual transitions in geometry, density, porosity, stiffness, etc., that mimic the biological extracellular matrix. The gradient structures in biological tissues play a major role in various functional and metabolic activities in the body. The designing of gradients in the scaffold can overcome the current challenges in the clinic compared to conventional scaffolds by exhibiting excellent penetration capacity for nutrients & cells, increased cellular adhesion, cell viability & differentiation, improved mechanical stability, and biocompatibility. In this review, the recent advancements in designing gradient scaffolds with desired biomimetic properties, and their implication in tissue regeneration applications have been briefly explained. Furthermore, the gradients in native tissues such as bone, cartilage, neuron, cardiovascular, skin and their specific utility in tissue regeneration have been discussed in detail. The insights from such advances using gradient-based scaffolds can widen the horizon for using gradient biomaterials in tissue regeneration applications.
Collapse
Affiliation(s)
- Ananya Pattnaik
- Laboratory of Biomaterials and Regenerative Medicine for Advanced Therapies, ICMR-Regional Medical Research Centre, Bhubaneswar, 751023, Odisha, India
| | - A Swaroop Sanket
- Laboratory of Biomaterials and Regenerative Medicine for Advanced Therapies, ICMR-Regional Medical Research Centre, Bhubaneswar, 751023, Odisha, India
| | - Sanghamitra Pradhan
- Department of Chemistry, Institute of Technical Education and Research, Siksha 'O' Anusandhan University, Bhubaneswar, 751030, Odisha, India
| | - Rajashree Sahoo
- Laboratory of Biomaterials and Regenerative Medicine for Advanced Therapies, ICMR-Regional Medical Research Centre, Bhubaneswar, 751023, Odisha, India
| | - Sudiptee Das
- Laboratory of Biomaterials and Regenerative Medicine for Advanced Therapies, ICMR-Regional Medical Research Centre, Bhubaneswar, 751023, Odisha, India
| | - Swarnaprbha Pany
- Laboratory of Biomaterials and Regenerative Medicine for Advanced Therapies, ICMR-Regional Medical Research Centre, Bhubaneswar, 751023, Odisha, India
| | - Timothy E L Douglas
- Engineering Department, Lancaster University, Lancaster, United Kingdom; Materials Science Institute, Lancaster University, Lancaster, United Kingdom
| | - Rambabu Dandela
- Department of Industrial and Engineering Chemistry, Institute of Chemical Technology, Indian Oil Odisha Campus, Bhubaneswar, Odisha, India
| | - Qiang Liu
- Advanced Drug Delivery and Regenerative Biomaterials Laboratory, Cardiovascular Institute, Stanford University School of Medicine, Department of Medicine, Stanford University, California, 94304, USA
| | - Jaykumar Rajadas
- Advanced Drug Delivery and Regenerative Biomaterials Laboratory, Cardiovascular Institute, Stanford University School of Medicine, Department of Medicine, Stanford University, California, 94304, USA; Department of Bioengineering and Therapeutic Sciences, University of California San Francusco (UCSF) School of Parmacy, California, USA
| | - Sanghamitra Pati
- Laboratory of Biomaterials and Regenerative Medicine for Advanced Therapies, ICMR-Regional Medical Research Centre, Bhubaneswar, 751023, Odisha, India
| | - Stefaan C De Smedt
- Laboratory of General Biochemistry and Physical Pharmacy, University of Ghent, Ghent, 9000, Belgium.
| | - Kevin Braeckmans
- Laboratory of General Biochemistry and Physical Pharmacy, University of Ghent, Ghent, 9000, Belgium
| | - Sangram Keshari Samal
- Laboratory of Biomaterials and Regenerative Medicine for Advanced Therapies, ICMR-Regional Medical Research Centre, Bhubaneswar, 751023, Odisha, India.
| |
Collapse
|
19
|
Kuyyamudi C, Menon SN, Sinha S. Precision of morphogen-driven tissue patterning during development is enhanced through contact-mediated cellular interactions. Phys Rev E 2023; 107:024407. [PMID: 36932610 DOI: 10.1103/physreve.107.024407] [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: 11/16/2021] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Cells in developing embryos reliably differentiate to attain location-specific fates, despite fluctuations in morphogen concentrations that provide positional information and in molecular processes that interpret it. We show that local contact-mediated cell-cell interactions utilize inherent asymmetry in the response of patterning genes to the global morphogen signal yielding a bimodal response. This results in robust developmental outcomes with a consistent identity for the dominant gene at each cell, substantially reducing the uncertainty in the location of boundaries between distinct fates.
Collapse
Affiliation(s)
- Chandrashekar Kuyyamudi
- The Institute of Mathematical Sciences, CIT Campus, Taramani, Chennai 600113, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400 094, India
| | - Shakti N Menon
- The Institute of Mathematical Sciences, CIT Campus, Taramani, Chennai 600113, India
| | - Sitabhra Sinha
- The Institute of Mathematical Sciences, CIT Campus, Taramani, Chennai 600113, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400 094, India
| |
Collapse
|
20
|
Saha S, Pradhan N, B N, Mahadevappa R, Minocha S, Kumar S. Cancer plasticity: Investigating the causes for this agility. Semin Cancer Biol 2023; 88:138-156. [PMID: 36584960 DOI: 10.1016/j.semcancer.2022.12.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/09/2022] [Accepted: 12/19/2022] [Indexed: 12/30/2022]
Abstract
Cancer is not a hard-wired phenomenon but an evolutionary disease. From the onset of carcinogenesis, cancer cells continuously adapt and evolve to satiate their ever-growing proliferation demands. This results in the formation of multiple subtypes of cancer cells with different phenotypes, cellular compositions, and consequently displaying varying degrees of tumorigenic identity and function. This phenomenon is referred to as cancer plasticity, during which the cancer cells exist in a plethora of cellular states having distinct phenotypes. With the advent of modern technologies equipped with enhanced resolution and depth, for example, single-cell RNA-sequencing and advanced computational tools, unbiased cancer profiling at a single-cell resolution are leading the way in understanding cancer cell rewiring both spatially and temporally. In this review, the processes and mechanisms that give rise to cancer plasticity include both intrinsic genetic factors such as epigenetic changes, differential expression due to changes in DNA, RNA, or protein content within the cancer cell, as well as extrinsic environmental factors such as tissue perfusion, extracellular milieu are detailed and their influence on key cancer plasticity hallmarks such as epithelial-mesenchymal transition (EMT) and cancer cell stemness (CSCs) are discussed. Due to therapy evasion and drug resistance, tumor heterogeneity caused by cancer plasticity has major therapeutic ramifications. Hence, it is crucial to comprehend all the cellular and molecular mechanisms that control cellular plasticity. How this process evades therapy, and the therapeutic avenue of targeting cancer plasticity must be diligently investigated.
Collapse
Affiliation(s)
- Shubhraneel Saha
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Nikita Pradhan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Neha B
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Ravikiran Mahadevappa
- Department of Biotechnology, School of Science, Gandhi Institute of Technology and Management, Deemed to be University, Bengaluru, Karnataka 562163, India
| | - Shilpi Minocha
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
| | - Saran Kumar
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
| |
Collapse
|
21
|
Bao M, Cornwall-Scoones J, Zernicka-Goetz M. Stem-cell-based human and mouse embryo models. Curr Opin Genet Dev 2022; 76:101970. [PMID: 35988317 PMCID: PMC10309046 DOI: 10.1016/j.gde.2022.101970] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 07/17/2022] [Accepted: 07/19/2022] [Indexed: 11/26/2022]
Abstract
Synthetic embryology aims to develop embryo-like structures from stem cells to provide new insight into early stages of mammalian development. Recent advances in synthetic embryology have highlighted the remarkable capacity of stem cells to self-organize under certain biochemical or biophysical stimulations, generating structures that recapitulate the fate and form of early mouse/human embryos, in which symmetry breaking, pattern formation, or proper morphogenesis can be observed spontaneously. Here we review recent progress on the design principles for different types of embryoids and discuss the impact of different biochemical and biophysical factors on the process of stem-cell self-organization. We also offer our thoughts about the principal future challenges.
Collapse
Affiliation(s)
- Min Bao
- California Institute of Technology, Division of Biology and Biological Engineering, 1200 E. California Boulevard, Pasadena, CA 91125, USA; Mammalian Embryo and Stem Cell Group, Department of Physiology, Development, and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK. https://twitter.com/@Min_Bao_
| | - Jake Cornwall-Scoones
- California Institute of Technology, Division of Biology and Biological Engineering, 1200 E. California Boulevard, Pasadena, CA 91125, USA; The Francis Crick Institute, London NW1 1AT, UK. https://twitter.com/@jake_cs_
| | - Magdalena Zernicka-Goetz
- California Institute of Technology, Division of Biology and Biological Engineering, 1200 E. California Boulevard, Pasadena, CA 91125, USA; Mammalian Embryo and Stem Cell Group, Department of Physiology, Development, and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK.
| |
Collapse
|
22
|
Habibey R, Rojo Arias JE, Striebel J, Busskamp V. Microfluidics for Neuronal Cell and Circuit Engineering. Chem Rev 2022; 122:14842-14880. [PMID: 36070858 PMCID: PMC9523714 DOI: 10.1021/acs.chemrev.2c00212] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The widespread adoption of microfluidic devices among the neuroscience and neurobiology communities has enabled addressing a broad range of questions at the molecular, cellular, circuit, and system levels. Here, we review biomedical engineering approaches that harness the power of microfluidics for bottom-up generation of neuronal cell types and for the assembly and analysis of neural circuits. Microfluidics-based approaches are instrumental to generate the knowledge necessary for the derivation of diverse neuronal cell types from human pluripotent stem cells, as they enable the isolation and subsequent examination of individual neurons of interest. Moreover, microfluidic devices allow to engineer neural circuits with specific orientations and directionality by providing control over neuronal cell polarity and permitting the isolation of axons in individual microchannels. Similarly, the use of microfluidic chips enables the construction not only of 2D but also of 3D brain, retinal, and peripheral nervous system model circuits. Such brain-on-a-chip and organoid-on-a-chip technologies are promising platforms for studying these organs as they closely recapitulate some aspects of in vivo biological processes. Microfluidic 3D neuronal models, together with 2D in vitro systems, are widely used in many applications ranging from drug development and toxicology studies to neurological disease modeling and personalized medicine. Altogether, microfluidics provide researchers with powerful systems that complement and partially replace animal models.
Collapse
Affiliation(s)
- Rouhollah Habibey
- Department of Ophthalmology, Universitäts-Augenklinik Bonn, University of Bonn, Ernst-Abbe-Straße 2, D-53127 Bonn, Germany
| | - Jesús Eduardo Rojo Arias
- Wellcome─MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, United Kingdom
| | - Johannes Striebel
- Department of Ophthalmology, Universitäts-Augenklinik Bonn, University of Bonn, Ernst-Abbe-Straße 2, D-53127 Bonn, Germany
| | - Volker Busskamp
- Department of Ophthalmology, Universitäts-Augenklinik Bonn, University of Bonn, Ernst-Abbe-Straße 2, D-53127 Bonn, Germany
| |
Collapse
|
23
|
Shen J, Liu F, Tang C. Scaling dictates the decoder structure. Sci Bull (Beijing) 2022; 67:1486-1495. [PMID: 36546192 DOI: 10.1016/j.scib.2022.06.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/06/2022] [Accepted: 06/13/2022] [Indexed: 01/07/2023]
Abstract
Despite fluctuations in embryo size within a species, the spatial gene expression pattern and hence the embryonic structure can nonetheless maintain the correct proportion to the embryo size. This is known as the scaling phenomenon. For morphogen-induced patterning of gene expression, the positional information encoded in the local morphogen concentrations is decoded by the downstream genetic network (the decoder). In this paper, we show that the requirement of scaling sets severe constraints on the geometric structure of such a local decoder, which in turn enables deduction of mutants' behavior and extraction of regulation information without going into any molecular details. We demonstrate that the Drosophila gap gene system achieves scaling in the way consistent with our theory-the decoder geometry required by scaling correctly accounts for the observed gap gene expression pattern in nearly all maternal morphogen mutants. Furthermore, the regulation logic and the coding/decoding strategy of the gap gene system can also be revealed from the decoder geometry. Our work provides a general theoretical framework for a large class of problems where scaling output is achieved by non-scaling inputs and a local decoder, as well as a unified understanding of scaling, mutants' behavior, and gene regulation for the Drosophila gap gene system.
Collapse
Affiliation(s)
- Jingxiang Shen
- Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Feng Liu
- Center for Quantitative Biology, Peking University, Beijing 100871, China; School of Physics, Peking University, Beijing 100871, China
| | - Chao Tang
- Center for Quantitative Biology, Peking University, Beijing 100871, China; School of Physics, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
| |
Collapse
|
24
|
Osteogenic Differentiation of Human Adipose-Derived Stem Cells Seeded on a Biomimetic Spongiosa-like Scaffold: Bone Morphogenetic Protein-2 Delivery by Overexpressing Fascia. Int J Mol Sci 2022; 23:ijms23052712. [PMID: 35269855 PMCID: PMC8911081 DOI: 10.3390/ijms23052712] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 01/27/2023] Open
Abstract
Human adipose-derived stem cells (hADSCs) have the capacity for osteogenic differentiation and, in combination with suitable biomaterials and growth factors, the regeneration of bone defects. In order to differentiate hADSCs into the osteogenic lineage, bone morphogenetic proteins (BMPs) have been proven to be highly effective, especially when expressed locally by route of gene transfer, providing a constant stimulus over an extended period of time. However, the creation of genetically modified hADSCs is laborious and time-consuming, which hinders clinical translation of the approach. Instead, expedited single-surgery gene therapy strategies must be developed. Therefore, in an in vitro experiment, we evaluated a novel growth factor delivery system, comprising adenoviral BMP-2 transduced fascia tissue in terms of BMP-2 release kinetics and osteogenic effects, on hADSCs seeded on an innovative biomimetic spongiosa-like scaffold. As compared to direct BMP-2 transduction of hADSCs or addition of recombinant BMP-2, overexpressing fascia provided a more uniform, constant level of BMP-2 over 30 days. Despite considerably higher BMP-2 peak levels in the comparison groups, delivery by overexpressing fascia led to a strong osteogenic response of hADSCs. The use of BMP-2 transduced fascia in combination with hADSCs may evolve into an expedited single-surgery gene transfer approach to bone repair.
Collapse
|
25
|
Jo J, Price-Whelan A, Dietrich LEP. Gradients and consequences of heterogeneity in biofilms. Nat Rev Microbiol 2022; 20:593-607. [PMID: 35149841 DOI: 10.1038/s41579-022-00692-2] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/11/2022] [Indexed: 12/15/2022]
Abstract
Historically, appreciation for the roles of resource gradients in biology has fluctuated inversely to the popularity of genetic mechanisms. Nevertheless, in microbiology specifically, widespread recognition of the multicellular lifestyle has recently brought new emphasis to the importance of resource gradients. Most microorganisms grow in assemblages such as biofilms or spatially constrained communities with gradients that influence, and are influenced by, metabolism. In this Review, we discuss examples of gradient formation and physiological differentiation in microbial assemblages growing in diverse settings. We highlight consequences of physiological heterogeneity in microbial assemblages, including division of labour and increased resistance to stress. Our impressions of microbial behaviour in various ecosystems are not complete without complementary maps of the chemical and physical geographies that influence cellular activities. A holistic view, incorporating these geographies and the genetically encoded functions that operate within them, will be essential for understanding microbial assemblages in their many roles and potential applications.
Collapse
Affiliation(s)
- Jeanyoung Jo
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Alexa Price-Whelan
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Lars E P Dietrich
- Department of Biological Sciences, Columbia University, New York, NY, USA.
| |
Collapse
|
26
|
Evenbratt H, Andreasson L, Bicknell V, Brittberg M, Mobini R, Simonsson S. Insights into the present and future of cartilage regeneration and joint repair. CELL REGENERATION (LONDON, ENGLAND) 2022; 11:3. [PMID: 35106664 PMCID: PMC8807792 DOI: 10.1186/s13619-021-00104-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 12/06/2021] [Indexed: 12/23/2022]
Abstract
Knee osteoarthritis is the most common joint disease. It causes pain and suffering for affected patients and is the source of major economic costs for healthcare systems. Despite ongoing research, there is a lack of knowledge regarding disease mechanisms, biomarkers, and possible cures. Current treatments do not fulfill patients' long-term needs, and it often requires invasive surgical procedures with subsequent long periods of rehabilitation. Researchers and companies worldwide are working to find a suitable cell source to engineer or regenerate a functional and healthy articular cartilage tissue to implant in the damaged area. Potential cell sources to accomplish this goal include embryonic stem cells, mesenchymal stem cells, or induced pluripotent stem cells. The differentiation of stem cells into different tissue types is complex, and a suitable concentration range of specific growth factors is vital. The cellular microenvironment during early embryonic development provides crucial information regarding concentrations of signaling molecules and morphogen gradients as these are essential inducers for tissue development. Thus, morphogen gradients implemented in developmental protocols aimed to engineer functional cartilage tissue can potentially generate cells comparable to those within native cartilage. In this review, we have summarized the problems with current treatments, potential cell sources for cell therapy, reviewed the progress of new treatments within the regenerative cartilage field, and highlighted the importance of cell quality, characterization assays, and chemically defined protocols.
Collapse
Affiliation(s)
| | - L. Andreasson
- Cline Scientific AB, SE-431 53 Mölndal, Sweden
- Institute of Biomedicine at Sahlgrenska Academy, Department of Clinical Chemistry and Transfusion Medicine, University of Gothenburg, SE-413 45 Gothenburg, Sweden
| | - V. Bicknell
- Cline Scientific AB, SE-431 53 Mölndal, Sweden
| | - M. Brittberg
- Cartilage Research Unit, University of Gothenburg, Region Halland Orthopaedics, Kungsbacka Hospital, S-434 80 Kungsbacka, Sweden
| | - R. Mobini
- Cline Scientific AB, SE-431 53 Mölndal, Sweden
| | - S. Simonsson
- Institute of Biomedicine at Sahlgrenska Academy, Department of Clinical Chemistry and Transfusion Medicine, University of Gothenburg, SE-413 45 Gothenburg, Sweden
| |
Collapse
|
27
|
Narita T, Kondo M, Oishi Y. Macroscopic Banding Pattern of Collagen Gel Formed by a Diffusion-Reaction Process. ACS OMEGA 2022; 7:1014-1020. [PMID: 35036765 PMCID: PMC8756805 DOI: 10.1021/acsomega.1c05601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 11/30/2021] [Indexed: 06/14/2023]
Abstract
Shapes and patterns observed in internal organs and tissues are reproducibly and robustly produced over a long distance (up to millimeters in length). The most fundamental remaining question is how these long geometries of shape and pattern form arise from the genetic message. Recent studies have demonstrated that extracellular matrix (ECM) critically participates as a structural foundation on which cells can organize and communicate. ECMs may be a key to understanding the underlying mechanisms of long-distance patterning and morphogenesis. However, previous studies in this field mainly focused on the complexes and interaction of cells and ECM. This paper pays particular attention to ECM and demonstrates that collagen, a major ECM component, natively possesses the reproducible and definite patterning ability reaching centimeter-scale length. The macroscopic pattern consists of striped transparent layers. The observation under crossed Nicols demonstrates that the layers consist of alternately arranged polarized and unpolarized parts. Confocal fluorescence microscopy studies revealed that the polarized and unpolarized segments include collagen-rich and -poor regions, respectively. The patterning process was proposed based on the Liesegang banding formation, which are mineral precipitation bands formed in hydrogel matrixes. These findings will give hints to the questions about long-distance cell alignment and provide new clues to artificially control cell placement over micron size in the field of regenerative medicine.
Collapse
|
28
|
Kuyyamudi C, Menon SN, Sinha S. Morphogen-regulated contact-mediated signaling between cells can drive the transitions underlying body segmentation in vertebrates. Phys Biol 2021; 19. [PMID: 34670199 DOI: 10.1088/1478-3975/ac31a3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/20/2021] [Indexed: 11/12/2022]
Abstract
We propose a unified mechanism that reproduces the sequence of dynamical transitions observed during somitogenesis, the process of body segmentation during embryonic development, that is invariant across all vertebrate species. This is achieved by combining inter-cellular interactions mediated via receptor-ligand coupling with global spatial heterogeneity introduced through a morphogen gradient known to occur along the anteroposterior axis. Our model reproduces synchronized oscillations in the gene expression in cells at the anterior of the presomitic mesoderm as it grows by adding new cells at its posterior, followed by travelling waves and subsequent arrest of activity, with the eventual appearance of somite-like patterns. This framework integrates a boundary-organized pattern formation mechanism, which uses positional information provided by a morphogen gradient, with the coupling-mediated self-organized emergence of collective dynamics, to explain the processes that lead to segmentation.
Collapse
Affiliation(s)
- Chandrashekar Kuyyamudi
- The Institute of Mathematical Sciences, CIT Campus, Taramani, Chennai 600113, India.,Homi Bhabha National Institute, Anushaktinagar, Mumbai 400 094, India
| | - Shakti N Menon
- The Institute of Mathematical Sciences, CIT Campus, Taramani, Chennai 600113, India
| | - Sitabhra Sinha
- The Institute of Mathematical Sciences, CIT Campus, Taramani, Chennai 600113, India.,Homi Bhabha National Institute, Anushaktinagar, Mumbai 400 094, India
| |
Collapse
|
29
|
Evans SD, Gehling JG, Erwin DH, Droser ML. Ediacara growing pains: Modular addition and development in Dickinsonia costata. PALEOBIOLOGY 2021; 97:10.1017/pab.2021.31. [PMID: 35001986 PMCID: PMC8740542 DOI: 10.1017/pab.2021.31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Constraining patterns of growth using directly observable and quantifiable characteristics can reveal a wealth of information regarding the biology of the Ediacara Biota - the oldest macroscopic, complex community forming organisms in the fossil record. However, these rely on individuals captured at an instant in time at various growth stages, and so different interpretations can be derived from the same material. Here we leverage newly discovered and well-preserved Dickinsonia costata Sprigg 1947 from South Australia, combined with hundreds of previously described specimens, to test competing hypotheses for the location of module addition. We find considerable variation in the relationship between the total number of modules and body size that cannot be explained solely by expansion and contraction of individuals. Patterns derived assuming new modules differentiated at the anterior result in numerous examples where the oldest module(s) must decrease in size with overall growth, potentially falsifying this hypothesis. Observed polarity as well as the consistent posterior location of defects and indentations support module formation at this end in D. costata. Regardless, changes in repeated units with growth share similarities with those regulated by morphogen gradients in metazoans today, suggesting that these genetic pathways were operating in Ediacaran animals.
Collapse
Affiliation(s)
- Scott D Evans
- Department of Geosciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - James G Gehling
- South Australia Museum, Adelaide, South Australia 5000, Australia
| | - Douglas H Erwin
- Department of Paleobiology MRC-121, National Museum of Natural History, Washington, DC 20013-7012, USA
| | - Mary L Droser
- Department of Earth and Planetary Sciences, University of California, Riverside, CA 92521, USA
| |
Collapse
|
30
|
Voronina AS, Pshennikova ES. mRNPs: Structure and role in development. Cell Biochem Funct 2021; 39:832-843. [PMID: 34212408 DOI: 10.1002/cbf.3656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 06/05/2021] [Accepted: 06/17/2021] [Indexed: 11/11/2022]
Abstract
In eukaryotic cells, mRNA molecules are coated with numerous RNA-binding proteins and so exist in ribonucleoproteins (mRNPs). The proteins associated with the mRNA regulate the fate of mRNA, including its localization, translation and decay. Before activation of translation, the mRNA does not display any template functions-it is masked. The coordinated activity of certain RNA-binding proteins determines the future fate of each mRNA individually. In embryo development, the temporal and spatial regulation of translation can cause a situation when the mRNA and the encoded protein are localized in different compartments and so the differentiation of the cells can be determined. The fundamentals of regulation of the mRNAs fate and functioning in nerves are similar to those already described for oo- and embryogenesis. Disorders in the mRNA masking and demasking result in the emergence of various diseases, in particular cancers and neuro-degenerative diseases.
Collapse
Affiliation(s)
- Anna S Voronina
- Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Elena S Pshennikova
- Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| |
Collapse
|
31
|
Kuyyamudi C, Menon SN, Sinha S. Contact-mediated cellular communication supplements positional information to regulate spatial patterning during development. Phys Rev E 2021; 103:062409. [PMID: 34271677 DOI: 10.1103/physreve.103.062409] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 06/02/2021] [Indexed: 12/12/2022]
Abstract
Development in multicellular organisms is marked by a high degree of spatial organization of the cells attaining distinct fates in the embryo. Recent experiments showing that suppression of intercellular interactions can alter the spatial patterns arising during development suggest that cell fates cannot be determined by the exclusive regulation of differential gene expression by morphogen gradients (the conventional view encapsulated in the French flag model). Using a mathematical model that describes the receptor-ligand interaction between cells in close physical proximity, we show that such intercellular signaling can regulate the process of selective gene expression within each cell, allowing information from the cellular neighborhood to influence the process by which the thresholds of morphogen concentration that dictate cell fates adaptively emerge. This results in local modulations of the positional cues provided by the global field set up by the morphogen, allowing interaction-mediated self-organized pattern formation to complement boundary-organized mechanisms in the context of development.
Collapse
Affiliation(s)
- Chandrashekar Kuyyamudi
- The Institute of Mathematical Sciences, CIT Campus, Taramani, Chennai 600113, India.,Homi Bhabha National Institute, Anushaktinagar, Mumbai 400 094, India
| | - Shakti N Menon
- The Institute of Mathematical Sciences, CIT Campus, Taramani, Chennai 600113, India
| | - Sitabhra Sinha
- The Institute of Mathematical Sciences, CIT Campus, Taramani, Chennai 600113, India.,Homi Bhabha National Institute, Anushaktinagar, Mumbai 400 094, India
| |
Collapse
|
32
|
Abstract
The Ediacara Biota preserves the oldest fossil evidence of abundant, complex metazoans. Despite their significance, assigning individual taxa to specific phylogenetic groups has proved problematic. To better understand these forms, we identify developmentally controlled characters in representative taxa from the Ediacaran White Sea assemblage and compare them with the regulatory tools underlying similar traits in modern organisms. This analysis demonstrates that the genetic pathways for multicellularity, axial polarity, musculature, and a nervous system were likely present in some of these early animals. Equally meaningful is the absence of evidence for major differentiation of macroscopic body units, including distinct organs, localized sensory machinery or appendages. Together these traits help to better constrain the phylogenetic position of several key Ediacara taxa and inform our views of early metazoan evolution. An apparent lack of heads with concentrated sensory machinery or ventral nerve cords in such taxa supports the hypothesis that these evolved independently in disparate bilaterian clades.
Collapse
Affiliation(s)
- Scott D Evans
- Department of Paleobiology MRC-121, National Museum of Natural History, Washington, DC 20013-7012, USA
| | - Mary L Droser
- Department of Earth and Planetary Sciences, University of California, Riverside, CA 92521, USA
| | - Douglas H Erwin
- Department of Paleobiology MRC-121, National Museum of Natural History, Washington, DC 20013-7012, USA
| |
Collapse
|
33
|
Slavkov I, Carrillo-Zapata D, Carranza N, Diego X, Jansson F, Kaandorp J, Hauert S, Sharpe J. Morphogenesis in robot swarms. Sci Robot 2021; 3:3/25/eaau9178. [PMID: 33141694 DOI: 10.1126/scirobotics.aau9178] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 11/14/2018] [Indexed: 12/31/2022]
Abstract
Morphogenesis allows millions of cells to self-organize into intricate structures with a wide variety of functional shapes during embryonic development. This process emerges from local interactions of cells under the control of gene circuits that are identical in every cell, robust to intrinsic noise, and adaptable to changing environments. Constructing human technology with these properties presents an important opportunity in swarm robotic applications ranging from construction to exploration. Morphogenesis in nature may use two different approaches: hierarchical, top-down control or spontaneously self-organizing dynamics such as reaction-diffusion Turing patterns. Here, we provide a demonstration of purely self-organizing behaviors to create emergent morphologies in large swarms of real robots. The robots achieve this collective organization without any self-localization and instead rely entirely on local interactions with neighbors. Results show swarms of 300 robots that self-construct organic and adaptable shapes that are robust to damage. This is a step toward the emergence of functional shape formation in robot swarms following principles of self-organized morphogenetic engineering.
Collapse
Affiliation(s)
- I Slavkov
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - D Carrillo-Zapata
- University of Bristol, Bristol, UK.,University of the West of England, Bristol, UK.,Bristol Robotics Laboratory, Bristol, UK
| | - N Carranza
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - X Diego
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,EMBL Barcelona, Barcelona, Spain
| | - F Jansson
- Centrum Wiskunde & Informatica (CWI), Amsterdam, Netherlands.,University of Amsterdam, Amsterdam, Netherlands
| | - J Kaandorp
- University of Amsterdam, Amsterdam, Netherlands
| | - S Hauert
- University of Bristol, Bristol, UK.,Bristol Robotics Laboratory, Bristol, UK
| | - J Sharpe
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,EMBL Barcelona, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| |
Collapse
|
34
|
Abstract
Precise characterization of a monolayer of two different biomolecules in a gradient pattern on a glass surface puts high demand on the method used. Some techniques can detect protein monolayers but not on a glass surface. Others can distinguish between different proteins but not identify a gradient pattern. Here, we used ToF-SIMS to validate the complete surface composition, checking all the necessary boxes. As these types of surfaces can dictate sensitive cell behaviors, the precision on a nanolevel is crucial, and to visualize and determine the molecular distribution become essential. The dual monolayer consisted of laminin 521 and one of three other biomolecules of different sizes, epidermal growth factor, growth differentiation factor 5, or bovine serum albumin, creating opposing gradient patterns. The resulting ToF-SIMS imaging and line scan data provided detailed information on the distribution of the adsorbed proteins.
Collapse
|
35
|
Diaz C, Puelles L. Developmental Genes and Malformations in the Hypothalamus. Front Neuroanat 2020; 14:607111. [PMID: 33324176 PMCID: PMC7726113 DOI: 10.3389/fnana.2020.607111] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 10/26/2020] [Indexed: 12/15/2022] Open
Abstract
The hypothalamus is a heterogeneous rostral forebrain region that regulates physiological processes essential for survival, energy metabolism, and reproduction, mainly mediated by the pituitary gland. In the updated prosomeric model, the hypothalamus represents the rostralmost forebrain, composed of two segmental regions (terminal and peduncular hypothalamus), which extend respectively into the non-evaginated preoptic telencephalon and the evaginated pallio-subpallial telencephalon. Complex genetic cascades of transcription factors and signaling molecules rule their development. Alterations of some of these molecular mechanisms acting during forebrain development are associated with more or less severe hypothalamic and pituitary dysfunctions, which may be associated with brain malformations such as holoprosencephaly or septo-optic dysplasia. Studies on transgenic mice with mutated genes encoding critical transcription factors implicated in hypothalamic-pituitary development are contributing to understanding the high clinical complexity of these pathologies. In this review article, we will analyze first the complex molecular genoarchitecture of the hypothalamus resulting from the activity of previous morphogenetic signaling centers and secondly some malformations related to alterations in genes implicated in the development of the hypothalamus.
Collapse
Affiliation(s)
- Carmen Diaz
- Department of Medical Sciences, School of Medicine and Institute for Research in Neurological Disabilities, University of Castilla-La Mancha, Albacete, Spain
| | - Luis Puelles
- Department of Human Anatomy and Psychobiology and IMIB-Arrixaca Institute, University of Murcia, Murcia, Spain
| |
Collapse
|
36
|
Minamihata K, Hamada Y, Kagawa G, Ramadhan W, Higuchi A, Moriyama K, Wakabayashi R, Goto M, Kamiya N. Dual-Functionalizable Streptavidin-SpyCatcher-Fused Protein-Polymer Hydrogels as Scaffolds for Cell Culture. ACS APPLIED BIO MATERIALS 2020; 3:7734-7742. [PMID: 35019513 DOI: 10.1021/acsabm.0c00940] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Hydrogels possessing the ability to control cell functions have great potential as artificial substrates for cell culture. Herein, we report dual-functionalizable protein-polymer hybrid hydrogels prepared by thiol oxidation catalyzed by horseradish peroxidase and a phenolic molecule. A chimera protein of streptavidin (SA) and the SpyCatcher protein, with a cysteine residue at its N-terminus, (C-SA-SC) was constructed and co-cross-linked with thiol-functionalized four-arm polyethylene glycol (PEG-SH) to obtain hydrogels possessing two orthogonal conjugation moieties. Hydrogel formation using C-SA-SC conjugated with biotinylated or SpyTagged functional molecules (premodification strategy) resulted in the formation of hydrogels with a uniform distribution of the functional molecules. Postmodification of the functional molecules of the C-SA-SC hydrogel with biotin or SpyTag could alter the three-dimensional (3D) spatial distribution of the functional molecules within the hydrogels depending on the mode of conjugation (SA/biotin or SpyCatcher/SpyTag), the size of the functional molecules, and the length of time of the modification. NIH-3T3 cells cultured on a C-SA-SC hydrogel, dual-functionalized with a biotinylated-Arg-Gly-Asp-Ser (RGDS) peptide and a basic fibroblast growth factor (bFGF) with SpyTag, showed cell adhesion to the PEG-SH-based hydrogels and cell morphological changes in response to the immobilized RGDS peptide and the bFGF. Moreover, the cells showed higher proliferation on the dual-functionalized C-SA-SC hydrogel than the cells cultured on hydrogels without either the RGDS peptide or the bFGF, demonstrating the benefits of dual-functionalizable hydrogels. The C-SA-SC hydrogel presented in this study is capable of being orthogonally functionalized by two different functional molecules with different 3D distributions of each molecule within the hydrogel and thus has the potential for use as a cell culturing scaffold for creating artificial cellular microstructures.
Collapse
Affiliation(s)
- Kosuke Minamihata
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yusei Hamada
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Genki Kagawa
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Wahyu Ramadhan
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Ayato Higuchi
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kousuke Moriyama
- Department of Chemical and Biological Engineering, National Institute of Technology, Sasebo College, Okishin-cho, Sasebo, Nagasaki 857-1193, Japan
| | - Rie Wakabayashi
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Masahiro Goto
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.,Division of Biotechnology, Center for Future Chemistry, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Noriho Kamiya
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.,Division of Biotechnology, Center for Future Chemistry, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| |
Collapse
|
37
|
York HM, Coyle J, Arumugam S. To be more precise: the role of intracellular trafficking in development and pattern formation. Biochem Soc Trans 2020; 48:2051-2066. [PMID: 32915197 PMCID: PMC7609031 DOI: 10.1042/bst20200223] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/24/2020] [Accepted: 08/26/2020] [Indexed: 02/07/2023]
Abstract
Living cells interpret a variety of signals in different contexts to elucidate functional responses. While the understanding of signalling molecules, their respective receptors and response at the gene transcription level have been relatively well-explored, how exactly does a single cell interpret a plethora of time-varying signals? Furthermore, how their subsequent responses at the single cell level manifest in the larger context of a developing tissue is unknown. At the same time, the biophysics and chemistry of how receptors are trafficked through the complex dynamic transport network between the plasma membrane-endosome-lysosome-Golgi-endoplasmic reticulum are much more well-studied. How the intracellular organisation of the cell and inter-organellar contacts aid in orchestrating trafficking, as well as signal interpretation and modulation by the cells are beginning to be uncovered. In this review, we highlight the significant developments that have strived to integrate endosomal trafficking, signal interpretation in the context of developmental biology and relevant open questions with a few chosen examples. Furthermore, we will discuss the imaging technologies that have been developed in the recent past that have the potential to tremendously accelerate knowledge gain in this direction while shedding light on some of the many challenges.
Collapse
Affiliation(s)
- Harrison M. York
- Monash Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC 3800, Australia
| | - Joanne Coyle
- Monash Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC 3800, Australia
| | - Senthil Arumugam
- Monash Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC 3800, Australia
- European Molecular Biological Laboratory Australia (EMBL Australia), Monash University, Melbourne, VIC 3800, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC 3800, Australia
| |
Collapse
|
38
|
Li X, Liu B, Pei B, Chen J, Zhou D, Peng J, Zhang X, Jia W, Xu T. Inkjet Bioprinting of Biomaterials. Chem Rev 2020; 120:10793-10833. [PMID: 32902959 DOI: 10.1021/acs.chemrev.0c00008] [Citation(s) in RCA: 230] [Impact Index Per Article: 57.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The inkjet technique has the capability of generating droplets in the picoliter volume range, firing thousands of times in a few seconds and printing in the noncontact manner. Since its emergence, inkjet technology has been widely utilized in the publishing industry for printing of text and pictures. As the technology developed, its applications have been expanded from two-dimensional (2D) to three-dimensional (3D) and even used to fabricate components of electronic devices. At the end of the twentieth century, researchers were aware of the potential value of this technology in life sciences and tissue engineering because its picoliter-level printing unit is suitable for depositing biological components. Currently inkjet technology has been becoming a practical tool in modern medicine serving for drug development, scaffold building, and cell depositing. In this article, we first review the history, principles and different methods of developing this technology. Next, we focus on the recent achievements of inkjet printing in the biological field. Inkjet bioprinting of generic biomaterials, biomacromolecules, DNAs, and cells and their major applications are introduced in order of increasing complexity. The current limitations/challenges and corresponding solutions of this technology are also discussed. A new concept, biopixels, is put forward with a combination of the key characteristics of inkjet printing and basic biological units to bring a comprehensive view on inkjet-based bioprinting. Finally, a roadmap of the entire 3D bioprinting is depicted at the end of this review article, clearly demonstrating the past, present, and future of 3D bioprinting and our current progress in this field.
Collapse
Affiliation(s)
- Xinda Li
- Biomanufacturing and Rapid Forming Technology Key Laboratory of Beijing, Department of Mechanical Engineering, Tsinghua University, Beijing 100084, People's Republic of China.,Key Laboratory for Advanced Materials Processing Technology, Ministry of Education, Department of Mechanical Engineering, Tsinghua University, Beijing 100084, People's Republic of China
| | - Boxun Liu
- Tsinghua-Berkeley Shenzhen Institute (TBSI), Tsinghua University, Shenzhen 518055, People's Republic of China
| | - Ben Pei
- Biomanufacturing and Rapid Forming Technology Key Laboratory of Beijing, Department of Mechanical Engineering, Tsinghua University, Beijing 100084, People's Republic of China.,Key Laboratory for Advanced Materials Processing Technology, Ministry of Education, Department of Mechanical Engineering, Tsinghua University, Beijing 100084, People's Republic of China
| | - Jianwei Chen
- Tsinghua-Berkeley Shenzhen Institute (TBSI), Tsinghua University, Shenzhen 518055, People's Republic of China.,East China Institute of Digital Medical Engineering, Shangrao 334000, People's Republic of China
| | - Dezhi Zhou
- Biomanufacturing and Rapid Forming Technology Key Laboratory of Beijing, Department of Mechanical Engineering, Tsinghua University, Beijing 100084, People's Republic of China.,Key Laboratory for Advanced Materials Processing Technology, Ministry of Education, Department of Mechanical Engineering, Tsinghua University, Beijing 100084, People's Republic of China
| | - Jiayi Peng
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, People's Republic of China
| | - Xinzhi Zhang
- Biomanufacturing and Rapid Forming Technology Key Laboratory of Beijing, Department of Mechanical Engineering, Tsinghua University, Beijing 100084, People's Republic of China.,Key Laboratory for Advanced Materials Processing Technology, Ministry of Education, Department of Mechanical Engineering, Tsinghua University, Beijing 100084, People's Republic of China
| | - Wang Jia
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, People's Republic of China
| | - Tao Xu
- Biomanufacturing and Rapid Forming Technology Key Laboratory of Beijing, Department of Mechanical Engineering, Tsinghua University, Beijing 100084, People's Republic of China.,Key Laboratory for Advanced Materials Processing Technology, Ministry of Education, Department of Mechanical Engineering, Tsinghua University, Beijing 100084, People's Republic of China.,Tsinghua-Berkeley Shenzhen Institute (TBSI), Tsinghua University, Shenzhen 518055, People's Republic of China
| |
Collapse
|
39
|
Periodic Oscillations of Myosin-II Mechanically Proofread Cell-Cell Connections to Ensure Robust Formation of the Cardiac Vessel. Curr Biol 2020; 30:3364-3377.e4. [DOI: 10.1016/j.cub.2020.06.041] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 05/14/2020] [Accepted: 06/12/2020] [Indexed: 01/08/2023]
|
40
|
Revaitis NT, Niepielko MG, Marmion RA, Klein EA, Piccoli B, Yakoby N. Quantitative analyses of EGFR localization and trafficking dynamics in the follicular epithelium. Development 2020; 147:dev183210. [PMID: 32680934 PMCID: PMC7438018 DOI: 10.1242/dev.183210] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 07/01/2020] [Indexed: 12/20/2022]
Abstract
To bridge the gap between qualitative and quantitative analyses of the epidermal growth factor receptor (EGFR) in tissues, we generated an sfGFP-tagged EGF receptor (EGFR-sfGFP) in Drosophila The homozygous fly appears similar to wild type with EGFR expression and activation patterns that are consistent with previous reports in the ovary, early embryo, and imaginal discs. Using ELISA, we quantified an average of 1100, 6200 and 2500 receptors per follicle cell (FC) at stages 8/9, 10 and ≥11 of oogenesis, respectively. Interestingly, the spatial localization of the EGFR to the apical side of the FCs at early stages depended on the TGFα-like ligand Gurken. At later stages, EGFR localized to basolateral positions of the FCs. Finally, we followed the endosomal localization of EGFR in the FCs. The EGFR colocalized with the late endosome, but no significant colocalization of the receptor was found with the early endosome. The EGFR-sfGFP fly is an exciting new resource for studying cellular localization and regulation of EGFR in tissues.
Collapse
Affiliation(s)
- Nicole T Revaitis
- Center for Computational and Integrative Biology, Rutgers, The State University of New Jersey, Camden, NJ 08103, USA
| | - Matthew G Niepielko
- New Jersey Center for Science, Technology & Mathematics, Kean University, Union, NJ 07083, USA
| | - Robert A Marmion
- Center for Computational and Integrative Biology, Rutgers, The State University of New Jersey, Camden, NJ 08103, USA
| | - Eric A Klein
- Center for Computational and Integrative Biology, Rutgers, The State University of New Jersey, Camden, NJ 08103, USA
- Department of Biology, Rutgers, The State University of New Jersey, Camden, NJ 08103, USA
| | - Benedetto Piccoli
- Center for Computational and Integrative Biology, Rutgers, The State University of New Jersey, Camden, NJ 08103, USA
- Department of Mathematical Sciences, Rutgers, The State University of New Jersey, Camden, NJ 08102, USA
| | - Nir Yakoby
- Center for Computational and Integrative Biology, Rutgers, The State University of New Jersey, Camden, NJ 08103, USA
- Department of Biology, Rutgers, The State University of New Jersey, Camden, NJ 08103, USA
| |
Collapse
|
41
|
Labibi B, Bashkurov M, Wrana JL, Attisano L. Modeling the Control of TGF-β/Smad Nuclear Accumulation by the Hippo Pathway Effectors, Taz/Yap. iScience 2020; 23:101416. [PMID: 32798968 PMCID: PMC7452192 DOI: 10.1016/j.isci.2020.101416] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 06/25/2020] [Accepted: 07/27/2020] [Indexed: 01/29/2023] Open
Abstract
Integration of transforming growth factor β (TGF-β) signals with those of other pathways allows for precise temporal and spatial control of gene expression patterns that drive development and homeostasis. The Hippo pathway nuclear effectors, Taz/Yap, interact with the TGF-β transcriptional mediators, Smads, to control Smad activity. Key to TGF-β signaling is the nuclear localization of Smads. Thus, to investigate the role of Taz/Yap in Smad nuclear accumulation, we developed mathematical models of Hippo and TGF-β cross talk. The models were based on experimental measurements of TGF-β-induced changes in Taz/Yap and Smad subcellular localization obtained using high-throughput immunofluorescence (IF) imaging in the mouse mammary epithelial cell line, EpH4. Bayesian MCMC DREAM parameter estimation was used to quantify the uncertainty in estimates of the kinetic parameters. Variation of the model parameters and statistical analysis show that our modeling predicts that Taz/Yap can alter TGF-β receptor activity and directly or indirectly act as nuclear retention factors. Taz/Yap modulate TGF-β-induced nuclear accumulation of Smad2/3 and Smad4 TGF-β does not affect Taz/Yap localization when Hippo activity is constant Taz/Yap loss may alter activity of both Receptor and Smad nuclear retention factors The mediator complex regulates Smad nuclear accumulation
Collapse
Affiliation(s)
- Bita Labibi
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Mikhail Bashkurov
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Jeffrey L Wrana
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Liliana Attisano
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada.
| |
Collapse
|
42
|
Optogenetic Rescue of a Patterning Mutant. Curr Biol 2020; 30:3414-3424.e3. [PMID: 32707057 DOI: 10.1016/j.cub.2020.06.059] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 04/13/2020] [Accepted: 06/17/2020] [Indexed: 12/14/2022]
Abstract
Animal embryos are patterned by a handful of highly conserved inductive signals. Yet, in most cases, it is unknown which pattern features (i.e., spatial gradients or temporal dynamics) are required to support normal development. An ideal experiment to address this question would be to "paint" arbitrary synthetic signaling patterns on "blank canvas" embryos to dissect their requirements. Here, we demonstrate exactly this capability by combining optogenetic control of Ras/extracellular signal-related kinase (ERK) signaling with the genetic loss of the receptor tyrosine-kinase-driven terminal signaling patterning in early Drosophila embryos. Blue-light illumination at the embryonic termini for 90 min was sufficient to rescue normal development, generating viable larvae and fertile adults from an otherwise lethal terminal signaling mutant. Optogenetic rescue was possible even using a simple, all-or-none light input that reduced the gradient of Erk activity and eliminated spatiotemporal differences in terminal gap gene expression. Systematically varying illumination parameters further revealed that at least three distinct developmental programs are triggered at different signaling thresholds and that the morphogenetic movements of gastrulation are robust to a 3-fold variation in the posterior pattern width. These results open the door to controlling tissue organization with simple optical stimuli, providing new tools to probe natural developmental processes, create synthetic tissues with defined organization, or directly correct the patterning errors that underlie developmental defects.
Collapse
|
43
|
Zonderland J, Rezzola S, Wieringa P, Moroni L. Fiber diameter, porosity and functional group gradients in electrospun scaffolds. Biomed Mater 2020; 15:045020. [DOI: 10.1088/1748-605x/ab7b3c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
44
|
Parameter estimation for a point-source diffusion-decay morphogen model. J Math Biol 2020; 80:2227-2255. [DOI: 10.1007/s00285-020-01494-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 02/08/2020] [Indexed: 10/24/2022]
|
45
|
Gordon NK, Chen Z, Gordon R, Zou Y. French flag gradients and Turing reaction-diffusion versus differentiation waves as models of morphogenesis. Biosystems 2020; 196:104169. [PMID: 32485350 DOI: 10.1016/j.biosystems.2020.104169] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/11/2020] [Accepted: 05/11/2020] [Indexed: 01/01/2023]
Abstract
The Turing reaction-diffusion model and the French Flag Model are widely accepted in the field of development as the best models for explaining embryogenesis. Virtually all current attempts to understand cell differentiation in embryos begin and end with the assumption that some combination of these two models works. The result may become a bias in embryogenesis in assuming the problem has been solved by these two-chemical substance-based models. Neither model is applied consistently. We review the differences between the French Flag, Turing reaction-diffusion model, and a mechanochemical model called the differentiation wave/cell state splitter model. The cytoskeletal cell state splitter and the embryonic differentiation waves was first proposed in 1987 as a combined physics and chemistry model for cell differentiation in embryos, based on empirical observations on urodele amphibian embryos. We hope that the development of theory can be advanced and observations relevant to distinguishing the embryonic differentiation wave model from the French Flag model and reaction-diffusion equations will be taken up by experimentalists. Experimentalists rely on mathematical biologists for theory, and therefore depend on them for what parameters they choose to measure and ignore. Therefore, mathematical biologists need to fully understand the distinctions between these three models.
Collapse
Affiliation(s)
| | - Zhan Chen
- Department of Mathematical Sciences, Georgia Southern University, Statesboro, GA, USA.
| | - Richard Gordon
- Gulf Specimen Marine Laboratory & Aquarium, 222 Clark Drive, Panacea, FL, 32346, USA; C.S. Mott Center for Human Growth & Development, Department of Obstetrics & Gynecology, Wayne State University, 275 E. Hancock, Detroit, MI, 48201, USA.
| | - Yuting Zou
- Department of Mathematical Sciences, Georgia Southern University, Statesboro, GA, USA.
| |
Collapse
|
46
|
Kipryushina YO, Yakovlev KV. Maternal control of early patterning in sea urchin embryos. Differentiation 2020; 113:28-37. [PMID: 32371341 DOI: 10.1016/j.diff.2020.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 04/10/2020] [Accepted: 04/17/2020] [Indexed: 02/06/2023]
Abstract
Sea urchin development has been studied extensively for more than a century and considered regulative since the first experimental evidence. Further investigations have repeatedly supported this standpoint by revealing the presence of inductive mechanisms that alter cell fate decisions at early cleavage stages and flexibility of development in response to environmental conditions. Some features indicate that sea urchin development is not completely regulative, but actually includes determinative events. In 16-cell embryos, mesomeres and macromeres represent multipotency, while the cell fate of most vegetal micromeres is restricted. It is known that the mature sea urchin eggs are polarized by the asymmetrical distribution of some maternal mRNAs and proteins. Spatially-distributed maternal factors are necessary for the orientation of the primary animal-vegetal axis, which is established by both maternal and zygotic mechanisms later in development. The secondary dorsal-ventral axis is conditionally specified later in development. Dorsal-ventral polarity is very liable during the early cleavages, though more recent data argue that its direction may be oriented by maternal asymmetry. In this review, we focus on the role of maternal factors in initial embryonic patterning during the first cleavages of sea urchin embryos before activation of the embryonic genome.
Collapse
Affiliation(s)
- Yulia O Kipryushina
- Laboratory of Cytotechnology, National Scientific Center of Marine Biology, Far Eastern Branch of the Russian Academy of Sciences, Palchevsky St. 17, 690041, Vladivostok, Russia
| | - Konstantin V Yakovlev
- Laboratory of Cytotechnology, National Scientific Center of Marine Biology, Far Eastern Branch of the Russian Academy of Sciences, Palchevsky St. 17, 690041, Vladivostok, Russia; Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.
| |
Collapse
|
47
|
Li Y, Zhang F, Jiang N, Liu T, Shen J, Zhang J. Decapentaplegic signaling regulates Wingless ligand production and target activation during
Drosophila
wing development. FEBS Lett 2020; 594:1176-1186. [DOI: 10.1002/1873-3468.13713] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 11/25/2019] [Accepted: 11/26/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Yunlong Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management College of Plant Protection China Agricultural University Beijing China
| | - Fengchao Zhang
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management College of Plant Protection China Agricultural University Beijing China
| | - Na Jiang
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management College of Plant Protection China Agricultural University Beijing China
| | - Tong Liu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management College of Plant Protection China Agricultural University Beijing China
| | - Jie Shen
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management College of Plant Protection China Agricultural University Beijing China
| | - Junzheng Zhang
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management College of Plant Protection China Agricultural University Beijing China
| |
Collapse
|
48
|
Takebayashi-Suzuki K, Suzuki A. Intracellular Communication among Morphogen Signaling Pathways during Vertebrate Body Plan Formation. Genes (Basel) 2020; 11:E341. [PMID: 32213808 PMCID: PMC7141137 DOI: 10.3390/genes11030341] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 03/18/2020] [Accepted: 03/19/2020] [Indexed: 12/25/2022] Open
Abstract
During embryonic development in vertebrates, morphogens play an important role in cell fate determination and morphogenesis. Bone morphogenetic proteins (BMPs) belonging to the transforming growth factor-β (TGF-β) family control the dorsal-ventral (DV) patterning of embryos, whereas other morphogens such as fibroblast growth factor (FGF), Wnt family members, and retinoic acid (RA) regulate the formation of the anterior-posterior (AP) axis. Activation of morphogen signaling results in changes in the expression of target genes including transcription factors that direct cell fate along the body axes. To ensure the correct establishment of the body plan, the processes of DV and AP axis formation must be linked and coordinately regulated by a fine-tuning of morphogen signaling. In this review, we focus on the interplay of various intracellular regulatory mechanisms and discuss how communication among morphogen signaling pathways modulates body axis formation in vertebrate embryos.
Collapse
Affiliation(s)
- Kimiko Takebayashi-Suzuki
- Amphibian Research Center, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Atsushi Suzuki
- Graduate School of Integrated Sciences for Life, Amphibian Research Center, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| |
Collapse
|
49
|
Lander AD, Nie Q, Sanchez-Tapia C, Simonyan A, Wan FYM. Regulatory feedback on receptor and non-receptor synthesis for robust signaling. Dev Dyn 2020; 249:383-409. [PMID: 32034817 DOI: 10.1002/dvdy.160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 01/16/2020] [Indexed: 12/22/2022] Open
Abstract
Elaborate regulatory feedback processes are thought to make biological development robust, that is, resistant to changes induced by genetic or environmental perturbations. How this might be done is still not completely understood. Previous numerical simulations on reaction-diffusion models of Dpp gradients in Drosophila wing imaginal disc have showed that feedback (of the Hill function type) on (signaling) receptors and/or non-(signaling) receptors are of limited effectiveness in promoting robustness. Spatial nonuniformity of the feedback processes has also been shown theoretically to lead to serious shape distortion and a principal cause for ineffectiveness. Through mathematical modeling and analysis, the present article shows that spatially uniform nonlocal feedback mechanisms typically modify gradient shape through a shape parameter (that does not change with location). This in turn enables us to uncover new multi-feedback instrument for effective promotion of robust signaling gradients.
Collapse
Affiliation(s)
- Arthur D Lander
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California.,Center for Complex Biological Systems (CCBS), University of California Irvine, Irvine, California
| | - Qing Nie
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California.,Center for Complex Biological Systems (CCBS), University of California Irvine, Irvine, California.,Department of Mathematics, University of California Irvine, Irvine, California.,NSF-Simon Center for Multiscale Cell Fate (CMCF), University of California Irvine, Irvine, California
| | | | - Aghavni Simonyan
- Department of Mathematics, University of California Irvine, Irvine, California.,Geffen Academy, UCLA, Los Angeles, California
| | - Frederic Y M Wan
- Department of Mathematics, University of California Irvine, Irvine, California
| |
Collapse
|
50
|
Gou X, E JC, Yang H, Sun D. Combined Single-Cell Manipulation and Chemomechanical Modeling to Probe Cell Migration Mechanism During Cell-to-Cell Interaction. IEEE Trans Biomed Eng 2019; 67:1474-1482. [PMID: 31484106 DOI: 10.1109/tbme.2019.2938569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Spatial presentations of chemical and mechanical information are key parameters for cell migration. However, previous theoretical and experimental studies focus on probing the mechanisms caused by a single type of stimulus, while ignoring the synergetic effects, especially for single cell migration during cell-to-cell interaction. Here we develop a chemomechanical model to assess the biochemical and biophysical modulators of single cell migration during cell-to-cell interaction. This model considers the stimulation of chemoattractant concentration gradient, influence of dynamic adhesion strength and relative motion between cells. The model is validated with single cell manipulation of leukemia cancer cell on stromal cell layer using optical tweezers. Both the modeling and experimental results demonstrate that cell migration velocity caused by chemotaxis can be biased by dynamic adhesion force, which is related to the retrograde flow of stromal cell layer. Besides, the biophysical modulators can influence the effect of drug treatment for specific signaling pathway. Our work provides a quantitative description of single cell migration in a complex environment that is close to realistic in vivo situation and is useful for further exploration of cell signaling pathway during cell-to-cell interactions for investigation of potential therapeutic strategy.
Collapse
|