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Article: Evaluation of Hi-C sequencing for the detection of gene fusions in hematologic and solid pediatric cancer samples.

Schmitt, Anthony D / Sikkink, Kristin / Ahmed, Atif A / Melnyk, Shadi / Reid, Derek / Van Meter, Logan / Guest, Erin M / Lansdon, Lisa A / Pastinen, Tomi / Pushel, Irina / Yoo, Byunggil / Farooqi, Midhat S

medRxiv : the preprint server for health sciences

2024

Abstract: HiC sequencing is a DNA-based next-generation sequencing method that preserves the 3D conformation of the genome and has shown promise in detecting genomic rearrangements in translational research studies. To evaluate HiC as a potential clinical ... ...

Abstract	HiC sequencing is a DNA-based next-generation sequencing method that preserves the 3D conformation of the genome and has shown promise in detecting genomic rearrangements in translational research studies. To evaluate HiC as a potential clinical diagnostic platform, analytical concordance with routine laboratory testing was assessed using primary pediatric leukemia and sarcoma specimens previously positive for clinically significant genomic rearrangements. Archived specimen types tested included viable and nonviable frozen leukemic cells, as well as formalin-fixed paraffin-embedded (FFPE) tumor tissues. Initially, pediatric acute myeloid leukemia (AML) and alveolar rhabdomyosarcoma (A-RMS) specimens with known genomic rearrangements were subjected to HiC analysis to assess analytical concordance. Subsequently, a discovery cohort consisting of AML and acute lymphoblastic leukemia (ALL) cases with no known genomic rearrangements based on prior clinical diagnostic testing were evaluated to determine whether HiC could detect rearrangements. Using a standard sequencing depth of 50 million raw read-pairs per sample, or approximately 5X raw genomic coverage, 100% concordance was observed between HiC and previous clinical cytogenetic and molecular testing. In the discovery cohort, a clinically relevant gene fusion was detected in 45% of leukemia cases (5/11). This study demonstrates the value of HiC sequencing to medical diagnostic testing as it identified several clinically significant rearrangements, including those that might have been missed by current clinical testing workflows. Key points: HiC sequencing is a DNA-based next-generation sequencing method that preserves the 3D conformation of the genome, facilitating detection of genomic rearrangements.HiC was 100% concordant with clinical diagnostic testing workflows for detecting clinically significant genomic rearrangements in pediatric leukemia and rhabdomyosarcoma specimens.HiC detected clinically significant genomic rearrangements not previously detected by prior clinical cytogenetic and molecular testing.HiC performed well with archived non-viable and viable frozen leukemic cell samples, as well as archived formalin-fixed paraffin-embedded tumor tissue specimens.
Language	English
Publishing date	2024-05-12
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.05.10.24306838
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Article: Assessing Heterogeneity in the N-Telopeptides of Type I Collagen by Mass Spectrometry.

Darula, Zsuzsanna / McCabe, Maxwell C / Barrett, Alex / Schmitt, Lauren R / Maslanka, Mark D / Saviola, Anthony J / Orgel, Joseph / Burlingame, Alma / Staab-Weijnitz, Claudia A / Stenmark, Kurt / Weaver, Valerie / Chalkley, Robert J / Hansen, Kirk C

bioRxiv : the preprint server for biology

2024

Abstract: Collagen cross-links created by the lysyl oxidase and lysyl hydroxylase families of enzymes are a significant contributing factor to the biomechanical strength and rigidity of tissues, which in turn influence cell signaling and ultimately cell phenotype. ...

Abstract	Collagen cross-links created by the lysyl oxidase and lysyl hydroxylase families of enzymes are a significant contributing factor to the biomechanical strength and rigidity of tissues, which in turn influence cell signaling and ultimately cell phenotype. In the clinic, the proteolytically liberated N-terminal cross-linked peptide of collagen I (NTX) is used as a biomarker of bone and connective tissue turnover, which is altered in several disease processes. Despite the clinical utility of these collagen breakdown products, the majority of the cross-linked peptide species have not been identified in proteomic datasets. Here we evaluate several parameters for the preparation and identification of these peptides from the collagen I-rich Achilles tendon. Our refined approach involving chemical digestion for protein solubilization coupled with mass spectrometry allows for the identification of the NTX cross-links in a range of modification states. Based on the specificity of the enzymatic cross-linking reaction we utilized follow-up variable modification searches to facilitate identification with a wider range of analytical workflows. We then applied a spectral library approach to identify differences in collagen cross-links in bovine pulmonary hypertension. The presented method offers unique opportunities to understand extracellular matrix remodeling events in development, aging, wound healing, and fibrotic disease that modulate collagen architecture through lysyl-hydroxylase and lysyl-oxidase enzymes.
Language	English
Publishing date	2024-03-31
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.03.31.587441
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Article ; Online: Serum proteomic analysis in esophagectomy patients with postoperative delirium: A case-control study.

Khan, Sikandar H / Perkins, Anthony J / Jawaid, Samreen / Wang, Sophia / Lindroth, Heidi / Schmitt, Rebecca E / Doles, Jason / True, Jason D / Gao, Sujuan / Caplan, Gideon A / Twigg, Homer L / Kesler, Kenneth / Khan, Babar A

Heart & lung : the journal of critical care

2023 Volume 63, Page(s) 35–41

Abstract: Background: Postoperative delirium occurs in up to 80% of patients undergoing esophagectomy. We performed an exploratory proteomic analysis to identify protein pathways that may be associated with delirium post-esophagectomy.: Objectives: Identify ... ...

Abstract	Background: Postoperative delirium occurs in up to 80% of patients undergoing esophagectomy. We performed an exploratory proteomic analysis to identify protein pathways that may be associated with delirium post-esophagectomy. Objectives: Identify proteins associated with delirium and delirium severity in a younger and higher-risk surgical population. Methods: We performed a case-control study using blood samples collected from patients enrolled in a negative, randomized, double-blind clinical trial. English speaking adults aged 18 years or older, undergoing esophagectomy, who had blood samples obtained were included. Cases were defined by a positive delirium screen after surgery while controls were patients with negative delirium assessments. Delirium was assessed using Richmond Agitation Sedation Scale and Confusion Assessment Method for the Intensive Care Unit, and delirium severity was assessed by Delirium Rating Scale-Revised-98. Blood samples were collected pre-operatively and on post-operative day 1, and discovery proteomic analysis was performed. Between-group differences in median abundance ratios were reported using Wilcoxon-Mann-Whitney Odds (WMWodds Results: 52 (26 cases, 26 controls) patients were included in the study with a mean age of 64 (SD 9.6) years, 1.9% were females and 25% were African American. The median duration of delirium was 1 day (IQR: 1-2), and the median delirium/coma duration was 2.5 days (IQR: 2-4). Two proteins with greater relative abundance ratio in patients with delirium were: Coagulation factor IX (WMWodds: 1.89 95%CI: 1.0-4.2) and mannosyl-oligosaccharide 1,2-alpha-mannosidase (WMWodds: 2.4 95%CI: 1.03-9.9). Protein abundance ratios associated with mean delirium severity at postoperative day 1 were Complement C2 (Spearman r Conclusions: We identified changes in proteins associated with coagulation, inflammation, and protein handling; larger, follow-up studies are needed to confirm our hypothesis-generating findings.
MeSH term(s)	Adult ; Female ; Humans ; Middle Aged ; Male ; Emergence Delirium ; Case-Control Studies ; Delirium/etiology ; Delirium/epidemiology ; Esophagectomy/adverse effects ; Proteomics ; Intensive Care Units
Language	English
Publishing date	2023-09-23
Publishing country	United States
Document type	Randomized Controlled Trial ; Journal Article
ZDB-ID	193129-5
ISSN	1527-3288 ; 0147-9563
ISSN (online)	1527-3288
ISSN	0147-9563
DOI	10.1016/j.hrtlng.2023.09.009
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Article ; Online: Cure of intravascular NK/T-cell lymphoma of the central nervous system by allogeneic hematopoietic cell transplantation.

Meissner, Julia / Schmitt, Michael / Andrulis, Mindaugas / Schweizer, Leonille / Dietrich, Sascha / Alber, Bettina / Harting, Inga / Kurz, Felix T / Martens, Uwe M / Ho, Anthony D / Müller-Tidow, Carsten / Dreger, Peter

Bone marrow transplantation

2022 Volume 57, Issue 9, Page(s) 1451–1454

MeSH term(s)	Central Nervous System ; Hematopoietic Stem Cell Transplantation ; Humans ; Lymphoma, T-Cell, Peripheral
Language	English
Publishing date	2022-06-09
Publishing country	England
Document type	Letter ; Research Support, Non-U.S. Gov't
ZDB-ID	632854-4
ISSN	1476-5365 ; 0268-3369 ; 0951-3078
ISSN (online)	1476-5365
ISSN	0268-3369 ; 0951-3078
DOI	10.1038/s41409-022-01734-2
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Zs.A 2168: Show issues

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Article ; Online: Architected fibrous scaffolds for engineering anisotropic tissues.

Reid, James Alexander / Dwyer, Kiera D / Schmitt, Phillip R / Soepriatna, Arvin H / Coulombe, Kareen Lk / Callanan, Anthony

Biofabrication

2021 Volume 13, Issue 4

Abstract: Mimicking the native three-dimensional microenvironment is of crucial importance when biofabricating a new healthcare material. One aspect of the native tissue that is often omitted when designing a suitable scaffold is its anisotropy. Not only is ... ...

Abstract	Mimicking the native three-dimensional microenvironment is of crucial importance when biofabricating a new healthcare material. One aspect of the native tissue that is often omitted when designing a suitable scaffold is its anisotropy. Not only is matching native mechanical properties important when designing implantable scaffolds or healthcare materials, but matching physiological structure is also important as many cell populations respond differently to fiber orientation. Therefore, novel aligned electrospun scaffolds with varying fiber angles and spacing of bundles were created and mechanically characterized. Through controlling the angle between the fibers in each layer of the scaffold, a range of different physiological anisotropic mechanical properties were achieved that encompasses values found in native tissues. Extrapolation of this mechanical data allowed for any native tissue's anisotropic Young's modulus to be mimicked by electrospinning fibers at a particular angle. These electrospun scaffolds were then incorporated with cell-laden hydrogels to create hybrid structures that contain the benefits of both scaffolding techniques with the ability to encapsulate cells in the hydrogel. To conclude, this study develops a novel bundled fiber scaffold that was architected to yield anisotropic properties matching native tissues.
MeSH term(s)	Anisotropy ; Biocompatible Materials ; Hydrogels ; Tissue Engineering ; Tissue Scaffolds
Chemical Substances	Biocompatible Materials ; Hydrogels
Language	English
Publishing date	2021-07-27
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2500944-8
ISSN	1758-5090 ; 1758-5082
ISSN (online)	1758-5090
ISSN	1758-5082
DOI	10.1088/1758-5090/ac0fc9
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Article ; Online: Genome-wide mapping and analysis of chromosome architecture.

Schmitt, Anthony D / Hu, Ming / Ren, Bing

Nature reviews. Molecular cell biology

2016 Volume 17, Issue 12, Page(s) 743–755

Abstract: Chromosomes of eukaryotes adopt highly dynamic and complex hierarchical structures in the nucleus. The three-dimensional (3D) organization of chromosomes profoundly affects DNA replication, transcription and the repair of DNA damage. Thus, a thorough ... ...

Abstract	Chromosomes of eukaryotes adopt highly dynamic and complex hierarchical structures in the nucleus. The three-dimensional (3D) organization of chromosomes profoundly affects DNA replication, transcription and the repair of DNA damage. Thus, a thorough understanding of nuclear architecture is fundamental to the study of nuclear processes in eukaryotic cells. Recent years have seen rapid proliferation of technologies to investigate genome organization and function. Here, we review experimental and computational methodologies for 3D genome analysis, with special focus on recent advances in high-throughput chromatin conformation capture (3C) techniques and data analysis.
MeSH term(s)	Animals ; Chromatin/ultrastructure ; Chromosome Mapping ; Chromosomes/ultrastructure ; Computer Simulation ; Humans ; Models, Molecular
Chemical Substances	Chromatin
Language	English
Publishing date	2016-09-01
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2031313-5
ISSN	1471-0080 ; 1471-0072
ISSN (online)	1471-0080
ISSN	1471-0072
DOI	10.1038/nrm.2016.104
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Zs.A 5446: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Taf2 mediates DNA binding of Taf14.

Klein, Brianna J / Feigerle, Jordan T / Zhang, Jibo / Ebmeier, Christopher C / Fan, Lixin / Singh, Rohit K / Wang, Wesley W / Schmitt, Lauren R / Lee, Thomas / Hansen, Kirk C / Liu, Wenshe R / Wang, Yun-Xing / Strahl, Brian D / Anthony Weil, P / Kutateladze, Tatiana G

Nature communications

2022 Volume 13, Issue 1, Page(s) 3177

Abstract: The assembly and function of the yeast general transcription factor TFIID complex requires specific contacts between its Taf14 and Taf2 subunits, however, the mechanism underlying these contacts remains unclear. Here, we determined the molecular and ... ...

Abstract	The assembly and function of the yeast general transcription factor TFIID complex requires specific contacts between its Taf14 and Taf2 subunits, however, the mechanism underlying these contacts remains unclear. Here, we determined the molecular and structural basis by which the YEATS and ET domains of Taf14 bind to the C-terminal tail of Taf2 and identified a unique DNA-binding activity of the linker region connecting the two domains. We show that in the absence of ligands the linker region of Taf14 is occluded by the surrounding domains, and therefore the DNA binding function of Taf14 is autoinhibited. Binding of Taf2 promotes a conformational rearrangement in Taf14, resulting in a release of the linker for the engagement with DNA and the nucleosome. Genetic in vivo data indicate that the association of Taf14 with both Taf2 and DNA is essential for transcriptional regulation. Our findings provide a basis for deciphering the role of individual TFIID subunits in mediating gene transcription.
MeSH term(s)	DNA/metabolism ; Gene Expression Regulation ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; TATA-Binding Protein Associated Factors/metabolism ; Transcription Factor TFIID/metabolism
Chemical Substances	Saccharomyces cerevisiae Proteins ; TAF14 protein, S cerevisiae ; TAF2 protein, S cerevisiae ; TATA-Binding Protein Associated Factors ; Transcription Factor TFIID ; DNA (9007-49-2)
Language	English
Publishing date	2022-06-08
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Intramural
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-30937-w
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Article: Elephant TP53-RETROGENE 9 induces transcription-independent apoptosis at the mitochondria.

Preston, Aidan J / Rogers, Aaron / Sharp, Miranda / Mitchell, Gareth / Toruno, Cristhian / Barney, Brayden B / Donovan, Lauren N / Bly, Journey / Kennington, Ryan / Payne, Emily / Iovino, Anthony / Furukawa, Gabriela / Robinson, Rosann / Shamloo, Bahar / Buccilli, Matthew / Anders, Rachel / Eckstein, Sarah / Fedak, Elizabeth A / Wright, Tanner /

Maley, Carlo C / Kiso, Wendy K / Schmitt, Dennis / Malkin, David / Schiffman, Joshua D / Abegglen, Lisa M

Cell death discovery

2023 Volume 9, Issue 1, Page(s) 66

Abstract: Approximately 20 TP53 retrogenes exist in the African and Asian elephant genomes (Loxodonta Africana, Elephas Maximus) in addition to a conserved TP53 gene that encodes a full-length protein. Elephant TP53-RETROGENE 9 (TP53-R9) encodes a p53 protein (p53- ...

Abstract	Approximately 20 TP53 retrogenes exist in the African and Asian elephant genomes (Loxodonta Africana, Elephas Maximus) in addition to a conserved TP53 gene that encodes a full-length protein. Elephant TP53-RETROGENE 9 (TP53-R9) encodes a p53 protein (p53-R9) that is truncated in the middle of the canonical DNA binding domain. This C-terminally truncated p53 retrogene protein lacks the nuclear localization signals and oligomerization domain of its full-length counterpart. When expressed in human osteosarcoma cells (U2OS), p53-R9 binds to Tid1, the chaperone protein responsible for mitochondrial translocation of human p53 in response to cellular stress. Tid1 expression is required for p53-R9-induced apoptosis. At the mitochondria, p53-R9 binds to the pro-apoptotic BCL-2 family member Bax, which leads to caspase activation, cytochrome c release, and cell death. Our data show, for the first time, that expression of this truncated elephant p53 retrogene protein induces apoptosis in human cancer cells. Understanding the molecular mechanism by which the additional elephant TP53 retrogenes function may provide evolutionary insight that can be utilized for the development of therapeutics to treat human cancers.
Language	English
Publishing date	2023-02-16
Publishing country	United States
Document type	Journal Article
ISSN	2058-7716
ISSN	2058-7716
DOI	10.1038/s41420-023-01348-7
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Article ; Online: Submyeloablative total body irradiation-based conditioning and allogeneic stem cell transplantation in high-risk myeloma with early progression after up-front autologous transplantation.

Mai, Elias K / Schmitt, Thomas / Radujkovic, Aleksandar / König, Laila / Goldschmidt, Hartmut / Ho, Anthony D / Luft, Thomas / Müller-Tidow, Carsten / Dreger, Peter / Hegenbart, Ute / Schönland, Stefan O

British journal of haematology

2021 Volume 196, Issue 1, Page(s) 244–248

MeSH term(s)	Disease Progression ; Hematopoietic Stem Cell Transplantation/methods ; Humans ; Multiple Myeloma/diagnosis ; Multiple Myeloma/mortality ; Multiple Myeloma/therapy ; Prognosis ; Retreatment ; Transplantation Conditioning/methods ; Transplantation, Autologous ; Transplantation, Homologous ; Treatment Outcome ; Whole-Body Irradiation/methods
Language	English
Publishing date	2021-08-24
Publishing country	England
Document type	Letter
ZDB-ID	80077-6
ISSN	1365-2141 ; 0007-1048
ISSN (online)	1365-2141
ISSN	0007-1048
DOI	10.1111/bjh.17779
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Uh III Zs.182: Show issues

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Article ; Online: Treatment of adult ALL patients with third-generation CD19-directed CAR T cells: results of a pivotal trial.

Schubert, Maria-Luisa / Schmitt, Anita / Hückelhoven-Krauss, Angela / Neuber, Brigitte / Kunz, Alexander / Waldhoff, Philip / Vonficht, Dominik / Yousefian, Schayan / Jopp-Saile, Lea / Wang, Lei / Korell, Felix / Keib, Anna / Michels, Birgit / Haas, Dominik / Sauer, Tim / Derigs, Patrick / Kulozik, Andreas / Kunz, Joachim / Pavel, Petra /

Laier, Sascha / Wuchter, Patrick / Schmier, Johann / Bug, Gesine / Lang, Fabian / Gökbuget, Nicola / Casper, Jochen / Görner, Martin / Finke, Jürgen / Neubauer, Andreas / Ringhoffer, Mark / Wolleschak, Denise / Brüggemann, Monika / Haas, Simon / Ho, Anthony D / Müller-Tidow, Carsten / Dreger, Peter / Schmitt, Michael

Journal of hematology & oncology

2023 Volume 16, Issue 1, Page(s) 79

Abstract: Background: Third-generation chimeric antigen receptor (CAR)-engineered T cells (CARTs) might improve clinical outcome of patients with B cell malignancies. This is the first report on a third-generation CART dose-escalating, phase-1/2 investigator- ... ...

Abstract	Background: Third-generation chimeric antigen receptor (CAR)-engineered T cells (CARTs) might improve clinical outcome of patients with B cell malignancies. This is the first report on a third-generation CART dose-escalating, phase-1/2 investigator-initiated trial treating adult patients with refractory and/or relapsed (r/r) acute lymphoblastic leukemia (ALL). Methods: Thirteen patients were treated with escalating doses of CD19-directed CARTs between 1 × 10 Results: For all patients, CART manufacturing was feasible. None of the patients developed any grade of Immune effector cell-associated neurotoxicity syndrome (ICANS) or a higher-grade (≥ grade III) catokine release syndrome (CRS). CART expansion and long-term CART persistence were evident in the peripheral blood (PB) of evaluable patients. At end of study on day 90 after CARTs, ten patients were evaluable for response: Eight patients (80%) achieved a complete remission (CR), including five patients (50%) with minimal residual disease (MRD)-negative CR. Response and outcome were associated with the administered CART dose. At 1-year follow-up, median overall survival was not reached and progression-free survival (PFS) was 38%. Median PFS was reached on day 120. Lack of CD39-expression on memory-like T cells was more frequent in CART products of responders when compared to CART products of non-responders. After CART administration, higher CD8 + and γδ-T cell frequencies, a physiological pattern of immune cells and lower monocyte counts in the PB were associated with response. Conclusion: In conclusion, third-generation CARTs were associated with promising clinical efficacy and remarkably low procedure-specific toxicity, thereby opening new therapeutic perspectives for patients with r/r ALL. Trial registration This trial was registered at www. Clinicaltrials: gov as NCT03676504.
MeSH term(s)	Humans ; Adult ; Neurotoxicity Syndromes ; Leukapheresis ; Adaptor Proteins, Signal Transducing ; Antigens, CD19/therapeutic use
Chemical Substances	cell-associated neurotoxicity ; Adaptor Proteins, Signal Transducing ; Antigens, CD19
Language	English
Publishing date	2023-07-22
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2429631-4
ISSN	1756-8722 ; 1756-8722
ISSN (online)	1756-8722
ISSN	1756-8722
DOI	10.1186/s13045-023-01470-0
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