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Lin C, Sniezek CM, McGann CD, Karki R, Giglio RM, Garcia BA, McFaline-Figeroa JL, Schweppe DK. Defining the heterogeneous molecular landscape of lung cancer cell responses to epigenetic inhibition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.23.592075. [PMID: 38853901 PMCID: PMC11160595 DOI: 10.1101/2024.05.23.592075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Epigenetic inhibitors exhibit powerful antiproliferative and anticancer activities. However, cellular responses to small-molecule epigenetic inhibition are heterogenous and dependent on factors such as the genetic background, metabolic state, and on-/off-target engagement of individual small-molecule compounds. The molecular study of the extent of this heterogeneity often measures changes in a single cell line or using a small number of compounds. To more comprehensively profile the effects of small-molecule perturbations and their influence on these heterogeneous cellular responses, we present a molecular resource based on the quantification of chromatin, proteome, and transcriptome remodeling due to histone deacetylase inhibitors (HDACi) in non-isogenic cell lines. Through quantitative molecular profiling of 10,621 proteins, these data reveal coordinated molecular remodeling of HDACi treated cancer cells. HDACi-regulated proteins differ greatly across cell lines with consistent (JUN, MAP2K3, CDKN1A) and divergent (CCND3, ASF1B, BRD7) cell-state effectors. Together these data provide valuable insight into cell-type driven and heterogeneous responses that must be taken into consideration when monitoring molecular perturbations in culture models.
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Affiliation(s)
- Chuwei Lin
- Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | | | | | - Rashmi Karki
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ross M. Giglio
- Biomedical Engineer, Columbia University, New York, NY 10027, USA
| | - Benjamin A. Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Devin K. Schweppe
- Genome Sciences, University of Washington, Seattle, WA 98105, USA
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA
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Clevenger AJ, Jha A, Moore E, Raghavan SA. Manipulating immune activity of macrophages: a materials and mechanics perspective. Trends Biotechnol 2024:S0167-7799(24)00187-2. [PMID: 39155172 DOI: 10.1016/j.tibtech.2024.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 07/15/2024] [Accepted: 07/16/2024] [Indexed: 08/20/2024]
Abstract
Macrophage immune cells exist on a plastic spectrum of phenotypes governed by their physical and biochemical environment. Controlling macrophage function to facilitate immunological regeneration or fighting pathology has emerged as a therapeutic possibility. The rate-limiting step in translating macrophage immunomodulation therapies has been the absence of fundamental knowledge of how physics and biochemistry in the macrophage microenvironment converge to inform phenotype. In this review we explore recent trends in bioengineered model systems that integrate physical and biochemical variables applied to macrophage mechanosensing and plasticity. We focus on how tuning of mechanical forces and biomaterial composition orchestrate macrophage function in physiological and pathological contexts. Ultimately, a broader understanding of stimuli-responsiveness in macrophages leads to informed design for future modulatory therapies.
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Affiliation(s)
- Abigail J Clevenger
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, USA
| | - Aakanksha Jha
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA
| | - Erika Moore
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA.
| | - Shreya A Raghavan
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, USA.
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Richbourg NR, Irakoze N, Kim H, Peyton SR. Outlook and opportunities for engineered environments of breast cancer dormancy. SCIENCE ADVANCES 2024; 10:eadl0165. [PMID: 38457510 PMCID: PMC10923521 DOI: 10.1126/sciadv.adl0165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 02/01/2024] [Indexed: 03/10/2024]
Abstract
Dormant, disseminated breast cancer cells resist treatment and may relapse into malignant metastases after decades of quiescence. Identifying how and why these dormant breast cancer cells are triggered into outgrowth is a key unsolved step in treating latent, metastatic breast cancer. However, our understanding of breast cancer dormancy in vivo is limited by technical challenges and ethical concerns with triggering the activation of dormant breast cancer. In vitro models avoid many of these challenges by simulating breast cancer dormancy and activation in well-controlled, bench-top conditions, creating opportunities for fundamental insights into breast cancer biology that complement what can be achieved through animal and clinical studies. In this review, we address clinical and preclinical approaches to treating breast cancer dormancy, how precisely controlled artificial environments reveal key interactions that regulate breast cancer dormancy, and how future generations of biomaterials could answer further questions about breast cancer dormancy.
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Affiliation(s)
- Nathan R. Richbourg
- Department of Chemical Engineering, University of Massachusetts Amherst, MA 01003, USA
| | - Ninette Irakoze
- Department of Chemical Engineering, University of Massachusetts Amherst, MA 01003, USA
| | - Hyuna Kim
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, MA 01003, USA
| | - Shelly R. Peyton
- Department of Chemical Engineering, University of Massachusetts Amherst, MA 01003, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, MA 01003, USA
- Department of Biomedical Engineering, University of Massachusetts Amherst Amherst, MA 01003, USA
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Molina-Aguilar C, Robles-Espinoza CD. Tackling the lack of diversity in cancer research. Dis Model Mech 2023; 16:dmm050275. [PMID: 37681401 PMCID: PMC10499025 DOI: 10.1242/dmm.050275] [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] [Indexed: 09/09/2023] Open
Abstract
Despite the clear benefit of studying biological samples from diverse genetic backgrounds and geographical locations, our current knowledge of disease is mostly derived from the study of European-descent individuals. In the cancer field, this is reflected in the poor representation of African and Amerindian/Latino samples in most large public data repositories. This lack of diversity is due to several reasons, but here we focus on (1) the lack of support for studies on non-European populations that are performed in low- and middle-income countries (LMICs), and (2) unequal partnerships between scientists in LMICs and those in high-income countries. We argue that expanding access to research funding, increasing the participation of underrepresented scientists in editorial boards and international conferences, facilitating the publication of studies conducted in these countries, and properly acknowledging LMIC researchers' contributions in publications and grant applications will promote equity for scientists working in LMICs. We envisage that this will translate to more impactful research in these countries, which will include more samples from diverse populations. For the cancer field, this will broaden our understanding of pathomechanisms and may help to improve the treatment of patients from all backgrounds.
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Affiliation(s)
- Christian Molina-Aguilar
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Santiago de Querétaro 76230, Mexico
| | - C. Daniela Robles-Espinoza
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Santiago de Querétaro 76230, Mexico
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
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Peyton SR, Platt MO, Cukierman E. Challenges and Opportunities Modeling the Dynamic Tumor Matrisome. BME FRONTIERS 2023; 4:0006. [PMID: 37849664 PMCID: PMC10521682 DOI: 10.34133/bmef.0006] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 11/28/2022] [Indexed: 10/19/2023] Open
Abstract
We need novel strategies to target the complexity of cancer and, particularly, of metastatic disease. As an example of this complexity, certain tissues are particularly hospitable environments for metastases, whereas others do not contain fertile microenvironments to support cancer cell growth. Continuing evidence that the extracellular matrix (ECM) of tissues is one of a host of factors necessary to support cancer cell growth at both primary and secondary tissue sites is emerging. Research on cancer metastasis has largely been focused on the molecular adaptations of tumor cells in various cytokine and growth factor environments on 2-dimensional tissue culture polystyrene plates. Intravital imaging, conversely, has transformed our ability to watch, in real time, tumor cell invasion, intravasation, extravasation, and growth. Because the interstitial ECM that supports all cells in the tumor microenvironment changes over time scales outside the possible window of typical intravital imaging, bioengineers are continuously developing both simple and sophisticated in vitro controlled environments to study tumor (and other) cell interactions with this matrix. In this perspective, we focus on the cellular unit responsible for upholding the pathologic homeostasis of tumor-bearing organs, cancer-associated fibroblasts (CAFs), and their self-generated ECM. The latter, together with tumoral and other cell secreted factors, constitute the "tumor matrisome". We share the challenges and opportunities for modeling this dynamic CAF/ECM unit, the tools and techniques available, and how the tumor matrisome is remodeled (e.g., via ECM proteases). We posit that increasing information on tumor matrisome dynamics may lead the field to alternative strategies for personalized medicine outside genomics.
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Affiliation(s)
- Shelly R. Peyton
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA, USA
| | - Manu O. Platt
- Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Edna Cukierman
- Cancer Signaling & Microenvironment Program, Marvin and Concetta Greenberg Pancreatic Cancer Institute, Fox Chase Cancer Center, Temple Health, Philadelphia, PA, USA
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Abstract
The publication of Resource articles is essential for the dissemination of novel, or substantially enhanced, tools, techniques, disease models, datasets and resources. By sharing knowledge and resources in a globally accessible manner, we can support human disease research to accelerate the translation of fundamental discoveries to effective treatments or diagnostics for diverse patient populations. To promote and encourage excellence in Resource articles, Disease Models & Mechanisms (DMM) is launching a new 'Outstanding Resource Paper Prize'. To celebrate this, we highlight recent outstanding DMM Resource articles that have the ultimate goal of benefitting of human health.
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Affiliation(s)
- Kirsty M. Hooper
- The Company of Biologists, Bidder Building, Station Road, Histon, Cambridge CB24 9LF, UK
| | - Julija Hmeljak
- The Company of Biologists, Bidder Building, Station Road, Histon, Cambridge CB24 9LF, UK
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Lek M, Hmeljak J, Hooper KM. Genetic variance in human disease - modelling the future of genomic medicine. Dis Model Mech 2022; 15:275862. [PMID: 35771631 PMCID: PMC9254226 DOI: 10.1242/dmm.049700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Summary: DMM is launching a new Subject Focus on genetic variance in human disease. Here, we discuss this ongoing series of invited articles and reflect on advances in understanding the genotype–phenotype complexities in disease.
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Affiliation(s)
- Monkol Lek
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Julija Hmeljak
- The Company of Biologists, Bidder Building, Station Road, Cambridge CB24 9LF, UK
| | - Kirsty M Hooper
- The Company of Biologists, Bidder Building, Station Road, Cambridge CB24 9LF, UK
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