Molecular and Cellular Biology of Transplantation

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Physiology and Pathology".

Deadline for manuscript submissions: closed (31 March 2025) | Viewed by 429

Special Issue Editors


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Guest Editor
Lower Saxony Centre for Biomedical Engineering, Implant Research and Development (NIFE), Hannover Medical School, 30625 Hanover, Germany
Interests: xenotransplantation; regeneration; decellularization; heart valves; ex vivo lung perfusion (EVLP); lung transplantation

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Guest Editor
1. Department of Cardiac Surgery, University Hospital, LMU Munich, 81377 Munich, Germany
2. Munich Heart Alliance, German Center for Cardiovascular Research (DZHK), 81377 Munich, Germany
Interests: heart transplantation; pediatric cardiac surgery; lung transplantation

Special Issue Information

Dear Colleagues,

Despite the progress being made in gene and cell therapies, organ transplantation will continue to be the primary treatment option for end-stage organ failure. However, patients still face significant challenges, including a shortage of donor organs and a high risk of acute and chronic graft failure. In this context, this Special Issue will explore recent advancements in the field, including ex vivo organ perfusion, xenotransplantation and the application of regulatory cells such as Tregs and CAR Tregs, with a focus on overcoming or mitigating these shortcomings.

Dr. Robert Ramm
Prof. Dr. Sebastian G. Michel
Guest Editors

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Keywords

  • xeno- and allotransplantation
  • ex vivo perfusion
  • costimulatory blockade
  • CAR Treg
  • accommodation

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Published Papers (1 paper)

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Research

13 pages, 1739 KiB  
Article
CYTO-SV-ML: A Machine Learning Tool for Cytogenetic Structural Variant Analysis in Somatic Cell Type Using Genome Sequences
by Tao Zhang, Paul Auer, Stephen R. Spellman, Jing Dong, Wael Saber and Yung-Tsi Bolon
Life 2025, 15(6), 929; https://doi.org/10.3390/life15060929 - 9 Jun 2025
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Abstract
(1) Background: Although whole genome sequencing (WGS) has enabled the comprehensive analyses of structural variants (SVs), more accurate and efficient methods are needed to distinguish large somatic SVs (SV size ≥ 1 Mb) traditionally detected through cytogenetic testing from germline SVs. (2) Methods: [...] Read more.
(1) Background: Although whole genome sequencing (WGS) has enabled the comprehensive analyses of structural variants (SVs), more accurate and efficient methods are needed to distinguish large somatic SVs (SV size ≥ 1 Mb) traditionally detected through cytogenetic testing from germline SVs. (2) Methods: A customized machine learning pipeline (CYTO-SV-ML) under Snakemake automation workflow was developed with a user interface to identify somatic cytogenetic SVs in WGS data. And this tool was applied for characterizing structural variation profiles in the whole blood of patients with myelodysplastic syndromes (MDSs). Known SVs mapped from well-established open databases were split into training and validation subsets for an AUTO-ML machine learning model in a CYTO-SV-ML pipeline. (3) Results: The benchmarking performance of the CYTO-SV-ML pipeline on somatic cytogenetic SV classification displayed an area under the receiver operating characteristic curve (AUCROC) of 0.94 for translocations and 0.92 for non-translocations, a sensitivity of 0.83 for translocations and 0.85 for non-translocations, and a specificity of 0.96 for translocations and 0.82 for non-translocations. Our method (207 somatic cytogenetic SVs) outperformed a conventional SV calling pipeline (143 somatic cytogenetic SVs) in an independent validation of clinical cytogenetic records. In addition, the CYTO-SV-ML pipeline uncovered novel somatic cytogenetic SVs in 49 (89%) of 55 patients without successful clinical cytogenetic results. (4) Conclusions: Our study demonstrates the high-performance machine learning approach of CYTO-SV-ML on benchmarking SV classification from genomic sequencing data, and further validations of novel anomalies by orthogonal methods will be essential to unlock its full clinical potential of cytogenetic diagnostics. Full article
(This article belongs to the Special Issue Molecular and Cellular Biology of Transplantation)
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