MetNet

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SEEK ID: https://nextseek-dev.mit.edu/investigations/4

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Created: 21st Jan 2026 at 15:07

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Projects (1)
Studies (10)
Assays (65)
SOPs (32)
Publications (12)

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Demo Demo

Projects: Published Data

Institutions: BMC-BioMicro Center (MIT)

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Showing 5 out of a possible 10 Studies Advanced Studies list for this Investigation with search and filtering

Myofibroblasts reduce angiogenesis and vasculogenesis in a vascularized microphysiological model of lung fibrosis

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Demo Demo

Elena Cambria, Adriana Blazeski, Eunkyung Clare Ko, Tran Thai, Shania Dantes, David A. Barbie, Sarah E. Shelton, Roger D. Kamm

https://www.biorxiv.org/content/10.1101/2025.01.10.632378v1

Abstract: Lung fibrosis, characterized by chronic and progressive scarring, has no cure. Hallmarks are the accumulation of myofibroblasts and extracellular matrix, as well as vascular remodeling. The crosstalk between myofibroblasts and vasculature is poorly understood, with ...

Submitter: Demo Demo

Investigation: MetNet

Assays: ELISA - Data Linked, Imaging - Data Linked, Imaging Analysis - Data Linked, Luminex - Data Linked, Microfluidic Network Formation - Metadata, RNA Extraction - Metadata, Real Time RT-PCR - Data Linked

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Created: 22nd Jan 2026 at 20:17

Remodeling of self-assembled microvascular networks under long term flow

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Marie Floryan, Elena Cambria, Adriana Blazeski, Mark F. Coughlin, Zhengpeng Wan, Giovanni Offeddu, Vinayak Vinayak, Aayush Kant, Vivek Shenoy, Roger D. Kamm

DOI:

Abstract: The incorporation of a functional perfusable microvascular network (MVN) is a common requirement for most organ on-chip-models. Long-term perfusion of MVNs is often required for the maturation of organ phenotypes and disease pathologies and to model the transport of cells and drugs entering ...

Submitter: Demo Demo

Investigation: MetNet

Assays: All Metadata, Cell Extraction - Metadata, Cytokine Luminex - Data Linked, Gene Expression Analysis - Data Linked, Library Prep - Metadata, MVN Imaging Analysis - Data Linked, Mass Spectrometry Proteomics - Data Linked, Microfluidic Network Formation - Metadata, Microfluidic Network Imaging - Data Linked, Proteomics Analysis - Data Linked, RNA Extraction - Metadata, Short Read Sequencing - Data Linked

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Created: 22nd Jan 2026 at 20:16

Chemo-mechanical diffusion waves explain collective dynamics of immune cell podosomes

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Ze Gong, Koen van den Dries, Rodrigo A. Migueles-Ramírez, Paul W. Wiseman, Alessandra Cambi & Vivek B. Shenoy

DOI: https://doi.org/10.1038/s41467-023-38598-z

Abstract: Immune cells, such as macrophages and dendritic cells, can utilize podosomes, mechanosensitive actin-rich protrusions, to generate forces, migrate, and patrol for foreign antigens. Individual podosomes probe their microenvironment through periodic protrusion and retraction cycles (height ...

Submitter: Demo Demo

Investigation: MetNet

Assays: Dendritic Cell Preparation - Metadata, Imaging Analysis - Data Linked, Live Cell Imaging - Data Linked, Modeling - Data Linked

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Created: 21st Jan 2026 at 15:08

Confined cell migration along extracellular matrix space in vivo

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Oleksandr Chepizhkoa, Josep-Maria Armengol-Colladob, Stephanie Alexander, Esther Wagenae, Bettina Weigelin, Luca Giomi, Peter Friedl, Stefano Zapperi,Caterina A. M. La Porta

DOI: https://doi.org/10.1073/pnas.2414009121

Abstract: Cancer metastasis involves the collective migration of cancer cells in confined space, a problem that has been widely investigated in vitro. Here, we quantify the flow patterns of cancer cell as they invade tissue space and deform ...

Submitter: Demo Demo

Investigation: MetNet

Assays: Imaging Analysis - Data Linked, Intravital Microscopy

Snapshots: No snapshots

Created: 21st Jan 2026 at 15:08

Chromatin conformation, gene transcription, and nucleosome remodeling as an emergent system

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Luay M Almassalha 1 2, Marcelo Carignano 2 3, Emily Pujadas Liwag 2 4, Wing Shun Li 2 3 5, Ruyi Gong 2 3, Nicolas Acosta 2 3, Cody L Dunton 2 3, Paola Carrillo Gonzalez 2 3, Lucas M Carter 2 4, Rivaan Kakkaramadam 2 4, Martin Kröger 6, Kyle L MacQuarrie 7 8, Jane Frederick 2 3, I Chae Ye 2 3, Patrick Su 2 3, Tiffany Kuo 2 4, Karla I Medina 2 4, Josh A Pritchard 2 3, Andrew Skol 7, Rikkert Nap 2 3, Masato Kanemaki 9 10 11, Vinayak Dravid 5 12 13 14 15, Igal Szleifer 2 3 12, Vadim Backman 2 3 ...

Submitter: Demo Demo

Investigation: MetNet

Assays: Cell Culture - Metadata, Cell Imaging - Data Linked, Chromatin Sequencing Analysis - Data Linked, Imaging Analysis - Data Linked, Library Creation - Metadata, Modeling - Data Linked, Short Read Sequencing - Data Linked

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Created: 21st Jan 2026 at 15:08

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Microfluidic Device Creation - Metadata

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Submitter: Demo Demo

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: MetNet

Study: Impact of fibrinogen, fibrin thrombi and thromb...

Organisms: No organisms

SOPs: No SOPs

Data files: No Data files

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Created: 21st Jan 2026 at 15:11

Flow Cytometry - Data Linked

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Submitter: Demo Demo

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: MetNet

Study: Impact of fibrinogen, fibrin thrombi and thromb...

Organisms: No organisms

SOPs: No SOPs

Data files: No Data files

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Created: 21st Jan 2026 at 15:11

Device Imaging - Data Linked

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Submitter: Demo Demo

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: MetNet

Study: Impact of fibrinogen, fibrin thrombi and thromb...

Organisms: No organisms

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 21st Jan 2026 at 15:11

Flow Cytometry Analysis - Data Linked

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Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: MetNet

Study: Impact of fibrinogen, fibrin thrombi and thromb...

Organisms: No organisms

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 21st Jan 2026 at 15:11

Cancer Cell Extravasation Analysis - Data Linked

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Submitter: Demo Demo

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: MetNet

Study: Impact of fibrinogen, fibrin thrombi and thromb...

Organisms: No organisms

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 21st Jan 2026 at 15:11

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Showing 5 out of a possible 32 SOPs Advanced SOPs list for this Investigation with search and filtering

MF_Flow_Proteomics_Protocol

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Submitter: Demo Demo

Investigations: MetNet

Studies: Remodeling of self-assembled microvascular netw...

Assays: Mass Spectrometry Proteomics - Data Linked, Proteomics Analysis - Data Linked

Created: 23rd Jan 2026 at 18:04, Last updated: 23rd Jan 2026 at 18:04

MF_RNAseq

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Creators: None

Submitter: Demo Demo

Investigations: MetNet

Studies: Remodeling of self-assembled microvascular netw...

Assays: Cell Extraction - Metadata, Gene Expression Analysis - Data Linked, Library Prep - Metadata, RNA Extraction - Metadata, Short Read Sequencing - Data Linked

Created: 23rd Jan 2026 at 16:43, Last updated: 23rd Jan 2026 at 16:43

P.KAM-240712_V1_GFP_FACS.docx

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Submitter: Demo Demo

Investigations: MetNet

Studies: Polyploidy of MDA-MB-231 cells drives increased...

Assays: Fluorescence-Activated Cell Sorting - Data Linked

Created: 22nd Jan 2026 at 20:35, Last updated: 22nd Jan 2026 at 20:35

P.KAM-240129-V1_Cell-Culture-and-Tumor-Spheroid-Creation-iVas.docx

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Submitter: Demo Demo

Investigations: MetNet

Studies: Patient-specific vascularized tumor model: Bloc...

Assays: Cell Culture and Tumor Spheroid Creation - Meta...

Created: 22nd Jan 2026 at 20:34, Last updated: 22nd Jan 2026 at 20:34

MF_MVN_imaging

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Submitter: Demo Demo

Investigations: MetNet

Studies: Remodeling of self-assembled microvascular netw...

Assays: Microfluidic Network Imaging - Data Linked

Created: 22nd Jan 2026 at 20:30, Last updated: 22nd Jan 2026 at 20:30

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Showing 5 out of a possible 12 Publications Advanced Publications list for this Investigation with search and filtering

Remodeling of self-assembled microvascular networks under long term flow.

Published Data

Abstract (Expand)

The incorporation of a functional perfusable microvascular network (MVN) is a common requirement for most organ on-chip-models. Long-term perfusion of MVNs is often required for the maturation of organ … phenotypes and disease pathologies and to model the transport of cells and drugs entering organs. In our microphysiological system, we observe that flow can recover perfusion in regressed MVNs and maintain perfusable MVNs for at least 51 days. Throughout the 51 days, however, the MVNs are continuously remodeling to align with the direction of bulk flow and only appear to attain morphological homeostasis with the use of maintenance medium without growth factors. We observed that the flow resistance of the MVNs decreases over time, and using a computational model, we show that stable vessels have higher flow rates and velocities compared to regressing vessels. Cytokine analysis suggests that static conditions generate an inflammatory state, and that continuous flow reduces inflammation over an extended period. Finally, through bulk RNA sequencing we identify that both the endothelial and fibroblast cells are actively engaged in vascular and matrix remodeling due to flow and that these effects persist for at least 2 weeks. This MPS can be applied to study hemodynamically driven processes, such as metastatic dissemination or drug distribution, or to model long-term diseases previously not captured by MPS, such as chronic inflammation or aging-associated diseases.

Authors: M. Floryan, E. Cambria, A. Blazeski, M. F. Coughlin, Z. Wan, G. Offeddu, V. Vinayak, A. Kant, V. Shenoy, R. D. Kamm

Date Published: 18th Mar 2025

Publication Type: Journal

PubMed ID: 40166169

DOI: 10.1101/2025.03.17.643791

Citation: bioRxiv [Preprint]. 2025 Mar 18:2025.03.17.643791. doi: 10.1101/2025.03.17.643791.

Created: 25th Aug 2026 at 19:01

Wnt signaling modulates mechanotransduction in the epidermis to drive hair follicle regeneration.

Published Data

Abstract (Expand)

Most wounds form scars without hair follicles. However, in the wound-induced hair neogenesis (WIHN) model of skin regeneration, wounds regenerate hair follicles if tissue rigidity is optimal. Although … WIHN depends on Wnt signaling, whether Wnt performs a mechanoregulatory role that contributes to regeneration remains uncharacterized. Here, we demonstrate that Wnt signaling affects mechanosensitivity at both cellular and tissue levels to drive WIHN. Atomic force microscopy revealed an attenuated substrate rigidity response in epidermal but not dermal cells of healing wounds. Super-resolution microscopy and nanoneedle probing of intracellular compartments in live human keratinocytes revealed that Wnt-induced chromatin remodeling triggers a 10-fold drop in nuclear rigidity without jeopardizing the nucleocytoskeletal mechanical coupling. Mechanistically, Wnt signaling orchestrated a massive reorganization of actin architecture and recruited adherens junctions to generate a mechanical syncytium-a cohesive contractile unit with superior capacity for force coordination and collective durotaxis. Collectively, our findings unveil Wnt signaling's mechanoregulatory role that manipulates the machinery of mechanotransduction to drive regeneration.

Authors: A. S. W. Oak, A. Bagchi, M. J. Brukman, J. Toth, J. Ford, Y. Zheng, A. Nace, R. Yang, J. C. Hsieh, J. E. Hayden, G. Ruthel, A. Ray, E. Kim, V. B. Shenoy, G. Cotsarelis

Date Published: 21st Feb 2025

Publication Type: Journal

PubMed ID: 39970220

DOI: 10.1126/sciadv.adq0638

Citation: Sci Adv. 2025 Feb 21;11(8):eadq0638. doi: 10.1126/sciadv.adq0638. Epub 2025 Feb 19.

Created: 25th Aug 2026 at 19:25

Myofibroblasts reduce angiogenesis and vasculogenesis in a vascularized microphysiological model of lung fibrosis.

Published Data

Abstract (Expand)

Lung fibrosis, characterized by chronic and progressive scarring, has no cure. Hallmarks are the accumulation of myofibroblasts and extracellular matrix, as well as vascular remodeling. The crosstalk … between myofibroblasts and vasculature is poorly understood, with conflicting reports on whether angiogenesis and vessel density are increased or decreased in lung fibrosis. We developed a microphysiological system that recapitulates the pathophysiology of lung fibrosis and disentangles myofibroblast-vascular interactions. Lung myofibroblasts maintained their phenotype in 3D without exogenous TGF-beta and displayed anti-angiogenic and anti-vasculogenic activities when cultured with endothelial cells in a microfluidic device. These effects, including decreased endothelial sprouting, altered vascular morphology, and increased vascular permeability, were mediated by increased TGF-beta1 and reduced VEGF secretion. Pharmacological interventions targeting these cytokines restored vascular morphology and permeability, demonstrating the potential of this model to screen anti-fibrotic drugs. This system provides insights into myofibroblast-vascular crosstalk in lung fibrosis and offers a platform for therapeutic development.

Authors: E. Cambria, A. Blazeski, E. C. Ko, T. Thai, S. Dantes, D. A. Barbie, S. E. Shelton, R. D. Kamm

Date Published: 14th Jan 2025

Publication Type: Journal

PubMed ID: 39868191

DOI: 10.1101/2025.01.10.632378

Citation: bioRxiv [Preprint]. 2025 Jan 14:2025.01.10.632378. doi: 10.1101/2025.01.10.632378.

Created: 25th Aug 2026 at 18:58

Chromatin conformation, gene transcription, and nucleosome remodeling as an emergent system.

Published Data

Abstract (Expand)

In single cells, variably sized nanoscale chromatin structures are observed, but it is unknown whether these form a cohesive framework that regulates RNA transcription. Here, we demonstrate that the … human genome is an emergent, self-assembling, reinforcement learning system. Conformationally defined heterogeneous, nanoscopic packing domains form by the interplay of transcription, nucleosome remodeling, and loop extrusion. We show that packing domains are not topologically associated domains. Instead, packing domains exist across a structure-function life cycle that couples heterochromatin and transcription in situ, explaining how heterochromatin enzyme inhibition can produce a paradoxical decrease in transcription by destabilizing domain cores. Applied to development and aging, we show the pairing of heterochromatin and transcription at myogenic genes that could be disrupted by nuclear swelling. In sum, packing domains represent a foundation to explore the interactions of chromatin and transcription at the single-cell level in human health.

Authors: L. M. Almassalha, M. Carignano, E. P. Liwag, W. S. Li, R. Gong, N. Acosta, C. L. Dunton, P. C. Gonzalez, L. M. Carter, R. Kakkaramadam, M. Kroger, K. L. MacQuarrie, J. Frederick, I. C. Ye, P. Su, T. Kuo, K. I. Medina, J. A. Pritchard, A. Skol, R. Nap, M. Kanemaki, V. Dravid, I. Szleifer, V. Backman

Date Published: 10th Jan 2025

Publication Type: Journal

PubMed ID: 39792661

DOI: 10.1126/sciadv.adq6652

Citation: Sci Adv. 2025 Jan 10;11(2):eadq6652. doi: 10.1126/sciadv.adq6652. Epub 2025 Jan 10.

Created: 25th Aug 2026 at 18:56

Confined cell migration along extracellular matrix space in vivo.

Published Data

Abstract (Expand)

Collective migration of cancer cells is often interpreted using concepts derived from the physics of active matter, but the experimental evidence is mostly restricted to observations made in vitro. … Here, we study collective invasion of metastatic cancer cells injected into the mouse deep dermis using intravital multiphoton microscopy combined with a skin window technique and three-dimensional quantitative image analysis. We observe a multicellular but low-cohesive migration mode characterized by rotational patterns which self-organize into antiparallel persistent tracks with orientational nematic order. We analyze the deformations induced by the cells in the extracellular matrix and find broadly distributed strain bands with a prevalence of compression. A model of active nematic hydrodynamics is able to describe several statistical features of the experimentally observed flow, suggesting that collective cancer cell invasion can be interpreted as a nematic active fluid in the turbulent regime. Our results help elucidate the migration patterns of cancer cells in vivo and provide quantitative guidance for the development of realistic in vitro and in silico models for collective cell migration.

Authors: O. Chepizhko, J. M. Armengol-Collado, S. Alexander, E. Wagena, B. Weigelin, L. Giomi, P. Friedl, S. Zapperi, C. A. M. La Porta

Date Published: 7th Jan 2025

Publication Type: Journal

PubMed ID: 39793073

DOI: 10.1073/pnas.2414009121

Citation: Proc Natl Acad Sci U S A. 2025 Jan 7;122(1):e2414009121. doi: 10.1073/pnas.2414009121. Epub 2024 Dec 30.

Created: 25th Aug 2026 at 18:57

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