4.7 Editorial Material

The Proportion of Donor-Specific Cell-Free DNA in Blood as a Marker of Transplant Rejection: Not an Absolute

Journal

CLINICAL CHEMISTRY
Volume 66, Issue 10, Pages 1257-1258

Publisher

OXFORD UNIV PRESS INC
DOI: 10.1093/clinchem/hvaa199

Keywords

-

Ask authors/readers for more resources

Authors

I am an author on this paper
Click your name to claim this paper and add it to your profile.

Reviews

Primary Rating

4.7
Not enough ratings

Secondary Ratings

Novelty
-
Significance
-
Scientific rigor
-
Rate this paper

Recommended

Article Multidisciplinary Sciences

Uncovering transcriptional dark matter via gene annotation independent single-cell RNA sequencing analysis

Michael F. Z. Wang, Madhav Mantri, Shao-Pei Chou, Gaetano J. Scuderi, David W. McKellar, Jonathan T. Butcher, Charles G. Danko, Iwijn De Vlaminck

Summary: Conventional single-cell RNA sequencing analysis relies on genome annotations that may be incomplete or inaccurate especially for understudied organisms. Here the authors present a bioinformatic tool that leverages single-cell data to uncover biologically relevant transcripts beyond the best available genome annotation.

NATURE COMMUNICATIONS (2021)

Article Multidisciplinary Sciences

Spatiotemporal single-cell RNA sequencing of developing chicken hearts identifies interplay between cellular differentiation and morphogenesis

Madhav Mantri, Gaetano J. Scuderi, Roozbeh Abedini-Nassab, Michael F. Z. Wang, David McKellar, Hao Shi, Benjamin Grodner, Jonathan T. Butcher, Iwijn De Vlaminck

Summary: By utilizing single-cell and spatial transcriptomics in chicken hearts, the authors conducted a census of cellular interactions from early to late four-chambered heart stage, identifying a distinct epicardial-mesenchymal cell population with a migratory phenotype.

NATURE COMMUNICATIONS (2021)

Article Medical Laboratory Technology

Measurement Biases Distort Cell-Free DNA Fragmentation Profiles and Define the Sensitivity of Metagenomic Cell-Free DNA Sequencing Assays

Adrienne Chang, Omary Mzava, Joan S. Lenz, Alexandre P. Cheng, Philip Burnham, S. Timothy Motley, Crissa Bennett, John T. Connelly, Darshana M. Dadhania, Manikkam Suthanthiran, John R. Lee, Amy Steadman, Iwijn De Vlaminck

Summary: The choice of DNA isolation and library preparation methods has a significant impact on the sensitivity of metagenomic cfDNA sequencing, and the bias in fragment length distributions from different experimental procedures plays an important role in the sensitivity of metagenomic cfDNA sequencing. Standardization in sample preparation protocols is crucial for achieving substantial gains in the sensitivity of microbial and other short fragment recovery in liquid biopsy.

CLINICAL CHEMISTRY (2022)

Editorial Material Medical Laboratory Technology

Molecular Approaches to Transplant Monitoring; Is the Horizon Here?

Sean Agbor-Enoh, Michael Oellerich, Angela Wu, Philip F. Halloran, Iwijn De Vlaminck, Michael Keller

CLINICAL CHEMISTRY (2021)

Article Multidisciplinary Sciences

Cell-free DNA profiling informs all major complications of hematopoietic cell transplantation

Alexandre Pellan Cheng, Matthew Pellan Cheng, Conor James Loy, Joan Sesing Lenz, Kaiwen Chen, Sami Smalling, Philip Burnham, Kaitlyn Marie Timblin, Jose Luis Orejas, Emily Silverman, Paz Polak, Francisco M. Marty, Jerome Ritz, Iwijn De Vlaminck

Summary: Allogeneic hematopoietic cell transplantation (HCT) is an effective treatment for hematologic malignancies and immune disorders. This study shows that cell-free DNA (cfDNA) in blood can be used for monitoring posttransplant complications, including graft-versus-host disease (GVHD), infection, relapse of underlying disease, and graft failure. The study demonstrates the potential of cfDNA to improve the care of HCT recipients by enabling earlier detection and better prediction of these complications.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)

Article Biology

Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal muscle regeneration

David W. McKellar, Lauren D. Walter, Leo T. Song, Madhav Mantri, Michael F. Z. Wang, Iwijn De Vlaminck, Benjamin D. Cosgrove

Summary: The study integrates single-cell and -nuclear transcriptomic analyses of mouse skeletal muscle in different conditions and after injury, constructing a transcriptomic model of myogenesis that identifies rare transitional states and cell subtypes. This resource supports large-scale integration of single-cell transcriptomic data for biological discovery.

COMMUNICATIONS BIOLOGY (2021)

Article Multidisciplinary Sciences

A metagenomic DNA sequencing assay that is robust against environmental DNA contamination

Omary Mzava, Alexandre Pellan Cheng, Adrienne Chang, Sami Smalling, Liz-Audrey Djomnang Kounatse, Joan Sesing Lenz, Randy Longman, Amy Steadman, Luis G. Gomez-Escobar, Edward J. Schenck, Mirella Salvatore, Michael J. Satlin, Manikkam Suthanthiran, John R. Lee, Christopher E. Mason, Darshana Dadhania, Iwijn De Vlaminck

Summary: SIFT-seq is a robust metagenomic DNA sequencing assay that allows for the identification and removal of environmental DNA contamination introduced during sample preparation. It has been successfully applied in screening for low-burden microbial infections in blood and urine, identifying COVID-19 co-infections, characterizing the urinary microbiome, and identifying microbial DNA signatures of sepsis and inflammatory bowel disease in blood.

NATURE COMMUNICATIONS (2022)

Article Multidisciplinary Sciences

A Tead1-Apelin axis directs paracrine communication from myogenic to endothelial cells in skeletal muscle

Umji Lee, Pascal Stuelsatz, Sonia Karaz, David W. McKellar, Julie Russeil, Maria Deak, Iwijn De Vlaminck, Christoph Lepper, Bart Deplancke, Benjamin D. Cosgrove, Jerome N. Feige

Summary: This study identifies the regulation of Apelin by Tead1, with Tead1 playing an important role in myogenic cells and influencing Apln secretion, which in turn affects endothelial remodeling during muscle repair.

ISCIENCE (2022)

Article Biotechnology & Applied Microbiology

Spatial mapping of the total transcriptome by in situ polyadenylation

David W. McKellar, Madhav Mantri, Meleana M. Hinchman, John S. L. Parker, Praveen Sethupathy, Benjamin D. Cosgrove, Iwijn De Vlaminck

Summary: Spatial transcriptomics allows us to study the spatial context of gene expression. Current methods are limited to detecting a subset of RNA transcripts. By using enzymatic in situ polyadenylation of RNA, we are able to detect the full spectrum of RNAs, expanding the scope of research. Applying this approach, we studied skeletal muscle regeneration and viral-induced myocarditis, and made new discoveries.

NATURE BIOTECHNOLOGY (2023)

Article Multidisciplinary Sciences

Metagenomic DNA sequencing to quantify Mycobacterium tuberculosis DNA and diagnose tuberculosis

Adrienne Chang, Omary Mzava, Liz-Audrey Kounatse Djomnang, Joan Sesing Lenz, Philip Burnham, Peter Kaplinsky, Alfred Andama, John Connelly, Christine M. Bachman, Adithya Cattamanchi, Amy Steadman, Iwijn De Vlaminck

Summary: Metagenomic next-generation sequencing has the potential for tuberculosis diagnosis, but the diagnostic performance is influenced by the composition of the control population and the burden of nontuberculous mycobacterial DNA.

SCIENTIFIC REPORTS (2022)

Article Biotechnology & Applied Microbiology

Spatial total RNA-sequencing maps coding, noncoding and viral RNAs in tissues

David W. McKellar, Iwijn De Vlaminck

Summary: Spatial total RNA-sequencing (STRS) combines in situ polyadenylation with existing spatial transcriptomics technologies, providing a comprehensive view of the transcriptome in tissues. This technique was used to spatially map coding, noncoding and nonhost RNAs in skeletal muscle regeneration and viral myocarditis models.

NATURE BIOTECHNOLOGY (2023)

Article Urology & Nephrology

Peritoneal Effluent Cell-Free DNA Sequencing in Peritoneal Dialysis Patients With and Without Peritonitis

Philip Burnham, Fanny Chen, Alexandre P. Cheng, Vesh Srivatana, Lisa T. Zhang, Emmanuel Edusei, Shady Albakry, Brittany Botticelli, Xunxi Guo, Amanda Renaghan, Jeffrey Silberzweig, Darshana M. Dadhania, Joan S. Lenz, Michael Heyang, Iliyan D. Iliev, Joshua A. Hayden, Lars F. Westblade, Iwijn De Vlaminck, John R. Lee

Summary: This study examines the utility of metagenomic sequencing of peritoneal effluent cell-free DNA (cfDNA) for evaluating the peritoneal effluent in PD patients with and without peritonitis. The results show that metagenomic sequencing can detect and identify various pathogens in the peritoneal effluent of PD patients, including cases of culture-negative peritonitis.

KIDNEY MEDICINE (2022)

Article Engineering, Biomedical

Recent advances in tools to map the microbiome

Hao Shi, Benjamin Grodner, Iwijn De Vlaminck

Summary: Microbes thrive in diverse habitats, forming ecological niches with rich species diversity and complex spatial structure. Mapping microbial genes, transcripts, and metabolites spatially can provide a better understanding of microbiome structure and function, with significant implications for future microbiome research.

CURRENT OPINION IN BIOMEDICAL ENGINEERING (2021)

Article Medicine, Research & Experimental

Cell-free DNA tissues of origin by methylation profiling reveals significant cell, tissue, and organ-specific injury related to COVID-19 severity

Alexandre Pellan Cheng, Matthew Pellan Cheng, Wei Gu, Joan Sesing Lenz, Elaine Hsu, Erwin Schurr, Guillaume Bourque, Mathieu Bourgey, Jerome Ritz, Francisco M. Marty, Charles Y. Chiu, Donald C. Vinh, Iwijn De Vlaminck

Summary: The study developed a blood test to quantify cell-, tissue-, and organ-specific injury due to COVID-19, finding evidence of lung and liver injury and involvement of red blood cell progenitors. The concentration of cell-free DNA correlated with disease progression and was significantly increased in patients requiring intubation, suggesting the utility of cell-free DNA as an analyte for monitoring and studying COVID-19.
Article Respiratory System

Donor-derived, cell-free DNA levels by next-generation targeted sequencing are elevated in allograft rejection after lung transplantation

Kiran K. Khush, Iwijn De Vlaminck, Helen Luikart, David J. Ross, Mark R. Nicolls

Summary: This study measured dd-cfDNA in lung transplantation recipients, finding elevated levels in cases of acute cellular rejection and chronic lung allograft dysfunction. There was no significant difference in dd-cfDNA levels for antibody-mediated rejection and allograft infection compared to stable cases. A threshold of 0.85% for dd-cfDNA was determined as optimal for predicting rejection events with moderate sensitivity and specificity.

ERJ OPEN RESEARCH (2021)

No Data Available