Studies

Kathryn M. Yammine, Sophia Mirda Abularach, Michael Xiong, Seo-yeon Kim, Agata A. Bikovtseva, Vincent L. Butty, Richard P. Schiavoni, John F. Bateman, Shireen R. Lamandé, and Matthew D. Shoulders

A dbGaP Submission is underway and metadata will be updated at the completion of submission. The remaining of the data and metadata are available here.

DOI: 10.1101/2024.11.07.622468.

Abstract:

Objectives Mutations in the procollagen-II gene (COL2A1) ...

The data / metadata will be available ** online** at the time of paper acceptance. If you would like access prior to acceptance, please reach out to Lindsay Volk: (lvolk@mit.edu)

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 ...

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 ...

Patricia S. Grace, Joshua M. Peters, Jaimie Sixsmith, Richard Lu, Corinne Luedeman, Brooke A. Fenderson, Andrew Vickers, Matthew D. Slein, Edward B. Irvine, Tanya McKitrick, Mo-Hui Wei, Richard D. Cummings, Aaron Wallace, Lisa A. Cavacini, Alok Choudhary, Megan K. Proulx, Christopher Sundling, Gunilla Källenius, Rajko Reljic, Joel D. Ernst, Arturo Casadevall, Camille Locht, Abraham Pinter, Christopher M. Sasseti, Bryan D. Bryson, Sarah M. Fortune, Galit Alter

...

Joshua M. Peters, Hannah P. Gideon, Travis K. Hughes, Cal Gunnarson, Pauline Maiello, Douaa Mugahid, Sarah K. Nyquist, Joshua D. Bromley, Paul C. Blainey, Beth F. Junecko, Molly L. Nelson, Douglas A. Lauffenburger, Philana Ling Lin, JoAnne L. Flynn, Alex K. Shalek, Sarah M. Fortune, Joshua T. Mattila, Bryan D. Bryson

DOI: https://www.biorxiv.org/content/10.1101/2024.05.24.595747v1.full

Additional Datasets:

• More Metadata associated with these NHPs exists ...

Owen Leddy, Yufei Cui, Ryuhjin Ahn, Lauren Stopfer, Elizabeth Choe, Do Hun Kim, Malte Roerden, Stefani Spranger, Bryan D. Bryson & Forest M. White

DOI: https://www.nature.com/articles/s41596-024-01076-x#Sec43

Abstract: Vaccines and immunotherapies that target peptide–major histocompatibility complexes (peptide–MHCs) have the potential to address multiple unmet medical needs in cancer and infectious disease. Designing vaccines and immunotherapies to target ...

*Tigist Y Tamir 1,2,3,6, Shreya Chaudhary 1,6, Annie X Li 1,6, Sonia E Trojan 1,4,6 3 , Cameron T Flower 1,2,5,6, Paula Vo 7 , Yufei Cui 1,3,6, Jeffrey C Davis1,4,6, Rachit S Mukkamala 1,3,6 4 , Francesca N Venditti 1,6, Alissandra L Hillis 8 , Alex Toker 8 , Matthew G Vander Heiden 1,2,4,6,7 5 , Jessica B Spinelli 9 , Norman J Kennedy 9 , Roger J Davis 9 , and *Forest M White 1,2,3,5,6

Image

DOI: https://www.biorxiv.org/content/10.1101/2024.08.28.609894v1.full

Abstract: Coordination of adaptive ...

Zhewen Guo, Haosheng Feng, Timothy Swager

DOI: https://pubs.acs.org/doi/10.1021/acssensors.4c02462

Abstract: Herein, we present the development and evaluation of a molecularly imprinted polymer (MIP) sensor for the sensitive and selective detection of N-nitrosodimethylamine (NDMA) in aqueous environments. MIP coatings over electrochemically active electrodes enable NDMA detection with a notably low detection limit of 1.16 ppb. Our findings demonstrate that the ...

Megan K. Proulx, Christine D. Wiggins, Charlotte J. Reames, Claire Wu, Michael C. Kiritsy, Patricia Grace, Clare M. Smith, Cecelia S. Lindestam Arlehamn, Galit Alter, Douglas A. Lauffenburger, Christopher M. Sassetti

Training Data for the Model: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE267774

Abstract: While control of Mycobacterium tuberculosis (Mtb) infection is generally understood to require a Th1-immune response and IFN secretion, infection ...

Krista M. Pullen, Ryan Finethy, Seung-Hyun B. Ko, Charlotte J. Reames, Christopher M. Sassetti, Douglas A. Lauffenburger

DOI:

Abstract:Numerous studies have identified similarities in blood transcriptomic signatures of mouse tuberculosis (TB) models and human disease phenotypes, such as type 1 interferon (IFN) production and innate immune cell activation, yet the pathophysiology observed in murine infection does not recapitulate some of the hallmarks of human ...

_Andrew W. Simonson, Joseph J. Zeppa, Allison N. Bucsan, Michael C. Chao, Supriya Pokkali, Forrest Hopkins, Michael R. Chase, Andrew J. Vickers, Matthew S. Sutton, Caylin G. Winchell, Amy J. Myers, Cassaundra L. Ameel, Ryan Kelly, Ben Krouse, Luke E. Hood, Jiaxiang Li, Chelsea C. Lehman, Megha Kamath, Jaime Tomko, Mark A. Rodgers, Rachel Donlan, Harris Chishti, H. Jacob Borish, Edwin Klein, Charles A. Scanga, Sarah Fortune, Philana Ling Lin, Pauline Maiello, Mario Roederer, Patricia A. Darrah, ...

Satomi Hirose, Tatusya Osaki, Roger D. Kamm

Link to Publication: https://doi.org/10.1101/2024.06.28.601261

Abstract: Metastasis, the leading cause of cancer-related deaths, involves a complex cascade of events, including extravasation. Despite extensive research into metastasis, the mechanisms underlying extravasation remain unclear. Molecular targeted therapies have advanced cancer treatment, yet their efficacy is limited, prompting exploration into novel ...

Joshua M. Peters, Edward B. Irvine, Jacob M. Rosenberg, Marc H. Wadsworth II, Travis K. Hughes, Matthew Sutton, Sarah K. Nyquist, Joshua D. Bromley, Rajib Mondal, Mario Roederer, Robert A. Seder, Patricia A. Darrah, Galit Alter, JoAnne L. Flynn, Alex K. Shalek, Sarah M. Fortune, Bryan D. Bryson

DOI: https://www.science.org/doi/10.1126/sciadv.adq8229

Intradermal Bacillus Calmette-Guérin (BCG) is the most widely administered vaccine, but it does not sufficiently ...

Huu Tuan Nguyen, Nadia Gurvich, Mark Robert Gillrie, Giovanni Offeddu, Mouhita Humayun, Ellen L. Kan, Zhengpeng Wan, Mark Frederick Coughlin, Christie Zhang, Vivian Vu, Sharon Wei Ling Lee, Seng-Lai Tan, David Barbie, Jonathan Hsu, Roger D. Kamm

Link to Paper: https://www.sciencedirect.com/science/article/abs/pii/S0142961224002655

Abstract: Tumor-associated inflammation drives cancer progression and therapy resistance, often linked to the infiltration of ...

Leela RL Davies, Chuangqi Wang, Pia Steigler, Kathryn A Bowman, Stephanie Fischinger, Mark Hatherill, Michelle Fisher, Staney Kimbung Mbandi, Miguel Rodo, Tom HM Ottenhoff, Hazel M Dockrell, Jayne S Sutherland, Harriet Mayanja-Kizza, W Henry Boom, Gerhard Walzl, Stefan H.E. Kaufmann, Elisa Nemes, Thomas J Scriba, Douglas Lauffenburger, Galit Alter, Sarah M. Fortune.

Link to Paper: https://doi.org/10.1038/s41564-024-01678-x

Abstract: Antibody features vary ...

Joshua D. Bromley, Sharie Keanne C. Ganchua, Sarah K. Nyquist, Pauline Maiello, Michael Chao, H. Jacob Borish, Mark Rodgers, Jaime Tomko, Kara Kracinovsky, Douaa Mugahid, Son Nguyen, Dennis Wang, Jacob M. Rosenberg, Edwin C. Klein, Hannah P. Gideon, Roisin Floyd-O’Sullivan, Bonnie Berger, Charles A Scanga, Philana Ling Lin, Sarah M. Fortune, Alex K. Shalek, JoAnne L. Flynn

Link to Paper: https://www.cell.com/immunity/fulltext/S1074-7613(24)00375-3

Immunological ...

Michelle Chen, Elliot I. Corless, Bevin P. Engelward, Timothy M. Swager

Link to Paper: https://pubs.acs.org/doi/full/10.1021/acsomega.4c03959

Agglutination of liquid Janus emulsions creates optical signals that can be detected and quantified. This study reports the detection and quantitation of Interleukin-6 (IL-6) using emulsions functionalized at the water-organic interface with engineered hyperthermophilic affinity proteins (rcSso7d) derived from ...

Jessica C. Beard, Chi-Hsien Wang, Arun Sridharan, Robert G. Croy, John M. Essigmann, Timothy M. Swager

Link to Paper: https://doi.org/10.1021/acssensors.4c00927

N-Nitrosamines are contaminants found throughout the environment, including in drinking water, and many nitrosamines are likely potent carcinogens. Correspondingly, there is need for rapid and cost-effective in-field detection methods that can provide timely information about their contamination ...

Shu Wang, Amy J Myers, Edward B Irvine, Chuangqi Wang, Pauline Maiello, Mark A Rodgers, Jaime Tomko, Kara Kracinovsky, H. Jacob Borish, Michael C Chao, Douaa Mugahid, Patricia A. Darrah, Robert A. Seder, Mario Roederer, Charles A Scanga, Philana Ling Lin, Galit Alter, Sarah M Fortune, JoAnne L Flynn, Douglas A Lauffenburger

Paper Link: https://doi.org/10.1101/2024.04.13.589359

Link to Model Validation Datasets: https://fairdomhub.org/studies/1198

Abstract: ...

Giovanni S. Offeddu#, Elena Cambria#, Sarah E. Shelton, Kristina Haase, Zhengpeng Wan, Luca Possenti, Huu Tuan Nguyen, Mark R. Gillrie, Dean Hickman, Charles G. Knutson, and Roger D. Kamm

Abstract: Desmoplasia in breast cancer leads to heterogeneity in physical properties of the tissue, resulting in disparities in drug delivery and treatment efficacy among patients, thus contributing to high disease mortality. Personalized in vitro breast cancer models hold ...

Meng Sun*, Jolie M. Phan*, Nathan S. Kieswetter, Krystle K.Q. Yu, Malisa T. Smith, Huang Huang, Sanjana Gupta, Gerlinde Obermoser, Holden Terry Maecker, Akshaya Krishnan, Neha Gupta, Mary Rieck, Peter Acs, Mustafa Ghanizada, Shin-Heng Chiou, Purvesh Khatri, W. Henry Boom, Thomas R. Hawn, Catherine M. Stein, Harriet Mayanja-Kizza, Mark M. Davis*, Chetan Seshadri*

Abstract: A subset of individuals with a high probability of exposure to M. tuberculosis (M.tb) ...

Caylin G. Winchell, Sarah K. Nyquist, Michael C. Chao, Pauline Maiello, Amy J. Myers, Forrest Hopkins, Michael Chase, Hannah P. Gideon, Kush V. Patel, Joshua D. Bromley, Andrew W. Simonson, Roisin Floyd-O’Sullivan, Marc Wadsworth, Jacob M. Rosenberg, Rockib Uddin, Travis Hughes, Ryan J. Kelly, Josephine Griffo, Jaime Tomko, Edwin Klein, Bonnie Berger, Charles A. Scanga, Joshua Mattila, Sarah M. Fortune, Alex K. Shalek, Philana Ling Lin, JoAnne L. Flynn; CD8+ lymphocytes are critical for early ...

Huu Tuan Nguyen, Nicholas Pietraszek, Sarah E. Shelton, Kwabena Arthur, Roger D. Kamm

Link to Paper:

Abstract: Significance: Accurate cell segmentation and classification in 3 dimensional (3D) images are vital for studying live cell behavior and drug responses in 3D tissue culture. Evaluating diverse cell populations in 3D cell culture over time necessitates non-toxic staining methods, as specific fluorescence tags may not be suitable and immunofluorescence ...

Edward B. Irvine, Joshua M. Peters, Richard Lu, Patricia S. Grace, Jaimie Sixsmith, Aaron Wallace, Matthew Schneider, Sally Shin, Wiktor Karpinski, Jeff C. Hsiao, Esther van Woudenbergh, Arturo Casadevall, Bryan D. Bryson, Lisa Cavacini, Galit Alter, Sarah M. Fortune doi: https://doi.org/10.1101/2022.05.01.490220

Novel vaccination and therapeutic strategies are urgently needed to mitigate the tuberculosis (TB) epidemic. While extensive efforts have focused ...

Jing Ge, Le P. Ngo, Simran Kaushal, Ian J. Tay, Elina Thadhani, Jennifer E. Kay, Patrizia Mazzucato, Danielle N. Chow, Jessica L. Fessler, David M. Weingeist, Robert W. Sobol, Leona D. Samson, Scott R. Floyd, Bevin P. Engelward,*

Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8439179/

DNA damage can be cytotoxic and mutagenic, and it is directly linked to aging, cancer, and other diseases. To counteract the deleterious effects of DNA damage, cells have ...

Norah Owiti, Joshua Corrigan, Lee Pribyl, Jennifer Kay, Bevin Engelward

https://doi.org/10.3390/ijms231911776

The comet assay is a versatile assay for detecting DNA damage in eukaryotic cells. The assay can measure the levels of various types of damage, including DNA strand breaks, abasic sites and alkali-sensitive sites. Furthermore, the assay can also be modified to include purified DNA glycosylases so that alkylated and oxidized bases can be detected. The ...

Edward B Irvine, Patricia A Darrah, Shu Wang, Chuangqi Wang, Ryan P McNamara, Mario Roederer, Robert A Seder, Douglas A Lauffenburger, JoAnne L Flynn, Sarah M Fortune, Galit Alter

https://doi.org/10.1101/2023.07.31.551245

Altering the route of Bacille Calmette-Guérin (BCG) immunization from low-dose intradermal vaccination to high-dose intravenous (IV) vaccination resulted in a high level of protection against Mycobacterium tuberculosis ( Mtb ) infection, ...

Emmanouil Angelidakis, Sophia Chen, Shun Zhang, Zhengpeng Wan, Roger D. Kamm, Sarah E. Shelton

Link to Paper: https://doi.org/10.1002/adhm.202202984

A bidirectional association exists between metastatic dissemination and the hypercoagulable state associated with many types of cancer. As such, clinical studies have provided evidence that markers associated with elevated levels of coagulation and fibrinolysis correlate with decreased patient survival. However, ...