Biophysical informatics reveals distinctive phenotypic signatures and functional diversity of single-cell lineages DOI Creative Commons
Trevor Chan, Xingjian Zhang, Michael Mak

et al.

Bioinformatics, Journal Year: 2022, Volume and Issue: 39(1)

Published: Dec. 28, 2022

In this work, we present an analytical method for quantifying both single-cell morphologies and cell network topologies of tumor populations use it to predict 3D behavior.We utilized a supervised deep learning approach perform instance segmentation on label-free live images across wide range densities. We measured shape properties characterized 136 clones (SCCs) derived from the YUMM1.7 YUMMER1.7 mouse melanoma lines. Using unsupervised clustering algorithm, identified six distinct morphological subclasses. further observed differences in growth invasion dynamics subclasses vitro spheroid model. Compared existing methods 2D or phenotype, our requires less time, needs no specialized equipment, is capable much higher throughput, making ideal applications such as high-throughput drug screening clinical diagnosis.//github.com/trevor-chan/Melanoma_NetworkMorphology.Bioinformatics online.

Language: Английский

Compression drives diverse transcriptomic and phenotypic adaptations in melanoma DOI Creative Commons
Xingjian Zhang, Xin Shi, Dingyao Zhang

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(39)

Published: Sept. 18, 2023

Physical forces are prominent during tumor progression. However, it is still unclear how they impact and drive the diverse phenotypes found in cancer. Here, we apply an integrative approach to investigate of compression on melanoma cells. We bioinformatics screen for most significant compression-induced transcriptomic changes phenotypic responses. show that associated with both improvement worsening patient prognoses. Phenotypically, volumetric inhibits cell proliferation migration. It also induces organelle stress intracellular oxidative increases pigmentation malignant cells normal human melanocytes. Finally, have undergone become more resistant cisplatin treatment. Our findings indicate a double-edged sword progression drives evolution.

Language: Английский

Citations

9
Volumetric compression by heterogeneous scaffold embedding promotes cerebral organoid maturation and does not impede growth DOI Creative Commons
Xiaowei Tang, Zitian Wang, Davit Khutsishvili

et al.

Cell Systems, Journal Year: 2023, Volume and Issue: 14(10), P. 872 - 882.e3

Published: Oct. 1, 2023

Language: Английский

Citations

8
Microscopy methods to visualize nuclear organization in biomechanical studies DOI
Hannah Kim, Melike Lakadamyali

Current Opinion in Biomedical Engineering, Journal Year: 2024, Volume and Issue: 30, P. 100528 - 100528

Published: Feb. 16, 2024

Language: Английский

Citations

3
Cancer spreading patterns based on epithelial-mesenchymal plasticity DOI Creative Commons
Rui Wang, Zhaopeng Yan

Frontiers in Cell and Developmental Biology, Journal Year: 2024, Volume and Issue: 12

Published: April 11, 2024

Introduction: Metastasis is a major cause of cancer-related deaths, underscoring the necessity to discern rules and patterns cancer cell spreading. Epithelial-mesenchymal plasticity contributes aggressiveness metastasis. Despite establishing key determinants metastatic ability, comprehensive understanding underlying mechanism unknown. We aimed propose classification system for cells based on epithelial-mesenchymal plasticity, focusing hysteresis transition hybrid epithelial/mesenchymal phenotype. Methods: extensively reviewed concept specifically considering Results: In this review hypothesis article, especially phenotype, we proposed cells, indicating that with potential could be classified into four types: irreversible hysteresis, weak strong These types had varied biology, spreading features, prognoses. Discussion: Our results highlight offers insights diverse behaviors providing implications

Language: Английский

Citations

2
Volumetric compression for engineering living systems DOI
Yiwei Li, Ming Guo

Nature Reviews Bioengineering, Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 12, 2024

Language: Английский

Citations

2
Forces in stem cells and cancer stem cells DOI Creative Commons
Farhan Chowdhury, Bo Huang, Ning Wang

et al.

Cells and Development, Journal Year: 2022, Volume and Issue: 170, P. 203776 - 203776

Published: March 26, 2022

Endogenous and exogenous forces are critical in physiology pathology of the human body. Increasing evidence suggests that these forces, mechanics, force-associated signaling essential regulating functions living cells. Here we review advances understanding impact mechanics on fate embryonic stem cells, adult cancer cells pathways mechanotransduction Stem-cells based models useful how influence physiology, pathology, development, which is incompletely understood, especially for mammals. We highlight increasing efforts emerging favorable clinical outcomes mechanomedicine, application mechanobiology to medicine. Major progresses mechanobiology, pillar mechanomedicine mechanohealth (application health), pivotal life force making substantial medicine health.

Language: Английский

Citations

10
Application of sequential cyclic compression on cancer cells in a flexible microdevice DOI Creative Commons
Sevgi Önal, Maan M. Alkaisi, Volker Nock

et al.

PLoS ONE, Journal Year: 2023, Volume and Issue: 18(1), P. e0279896 - e0279896

Published: Jan. 5, 2023

Mechanical forces shape physiological structure and function within cell tissue microenvironments, during which cells strive to restore their or develop an adaptive mechanism maintain integrity depending on strength type of the mechanical loading. While some are shown experience permanent plastic deformation after a repetitive tensile loading unloading, impact such compression is yet be understood. As such, ability apply cyclic crucial for any experimental setup aimed at study taking place in microenvironments. Here, we demonstrate using microfluidic platform live actin SKOV-3 ovarian cancer cells. Live imaging cytoskeleton dynamics compressed was performed varying pressures applied sequentially ascending order compression. Additionally, recovery investigated by capturing nuclei profiles zero time 24 h-recovery end point assays. This range mild range. Results showed that phenotypical response with 20.8 kPa differed observably from 15.6 kPa. demonstrated aid capture differences behaviour as result being various physiologically relevant manner. Differences observed between fixed suggest exhibit deformations compression, proposed use prevent damage. Thus, biomechanical responses sequential could revealed flexible microdevice. this work, observation morphological, cytoskeletal nuclear non-compressed cells, controlled micro-scale live-cell imaging, fluorescent tagging assays, can give insights into mechanics

Language: Английский

Citations

6
Dynamics of Epithelial–Mesenchymal Plasticity: What Have Single-Cell Investigations Elucidated So Far? DOI Creative Commons
Seemadri Subhadarshini,

Joel Markus,

Sarthak Sahoo

et al.

ACS Omega, Journal Year: 2023, Volume and Issue: 8(13), P. 11665 - 11673

Published: March 22, 2023

Epithelial–mesenchymal plasticity (EMP) is a key driver of cancer metastasis and therapeutic resistance, through which cells can reversibly dynamically alter their molecular functional traits along the epithelial–mesenchymal spectrum. While in epithelial phenotype are usually tightly adherent, less metastatic, drug-sensitive, those hybrid epithelial/mesenchymal and/or mesenchymal state more invasive, migratory, drug-resistant, immune-evasive. Single-cell studies have emerged as powerful tool gaining new insights into dynamics EMP across various types. Here, we review many recent that employ single-cell analysis techniques to better understand both vitro vivo. These underlined plurality trajectories traverse during consequent heterogeneity phenotypes seen at preclinical clinical levels. They also demonstrate how diverse may exhibit hysteretic behavior rate such cell-state transitions depends on genetic/epigenetic background recipient cells, well dose duration EMP-inducing growth factors. Finally, discuss relationship between patient survival We present next set questions related could benefit much from observations pave way tackle phenotypic switching clinic.

Language: Английский

Citations

6
Population dynamics of EMT elucidates the timing and distribution of phenotypic intra-tumoral heterogeneity DOI Creative Commons
Annice Najafi, Mohit Kumar Jolly, Jason T. George

et al.

iScience, Journal Year: 2023, Volume and Issue: 26(7), P. 106964 - 106964

Published: June 5, 2023

The Epithelial-to-Mesenchymal Transition (EMT) is a hallmark of cancer metastasis and morbidity. EMT non-binary process, cells can be stably arrested en route to in an intermediate hybrid state associated with enhanced tumor aggressiveness worse patient outcomes. Understanding progression detail will provide fundamental insights into the mechanisms underlying metastasis. Despite increasingly available single-cell RNA sequencing (scRNA-seq) data that enable in-depth analyses at resolution, current inferential approaches are limited bulk microarray data. There thus great need for computational frameworks systematically infer predict timing distribution EMT-related states resolution. Here, we develop framework reliable inference prediction trajectories from scRNA-seq Our model utilized across variety applications

Language: Английский

Citations

6
Enhancing single-cell biology through advanced AI-powered microfluidics DOI Creative Commons
Zhaolong Gao, Yiwei Li

Biomicrofluidics, Journal Year: 2023, Volume and Issue: 17(5)

Published: Sept. 1, 2023

Microfluidic technology has largely benefited both fundamental biological research and translational clinical diagnosis with its advantages in high-throughput, single-cell resolution, high integrity, wide-accessibility. Despite the merits we obtained from microfluidics last two decades, current requirement of intelligence biomedicine urges microfluidic to process big data more efficiently intelligently. Thus, readout based on direct detection signals either optics or electrics was not able meet requirement. The implementation artificial (AI) matches up large-scale usually high-throughput assays microfluidics. At same time, AI is multimodal datasets versatile devices, including images, videos, electric signals, sequences. Moreover, provides capability understand decipher rather than simply obtaining, which eventually facilitates many areas, cell type discovery, signaling, genetics, diagnosis. In this Perspective, will highlight recent advances employing for biology present an outlook future direction advanced algorithms.

Language: Английский

Citations

6