1
|
Michalska-Falkowska A, Niklinski J, Juhl H, Sulewska A, Kisluk J, Charkiewicz R, Ciborowski M, Ramlau R, Gryczka R, Piwkowski C, Kozlowski M, Miskiewicz B, Biecek P, Wnorowska K, Dzieciol-Anikiej Z, Sargsyan K, Naumnik W, Mroz R, Reszec-Gielazyn J. Applied Molecular-Based Quality Control of Biobanked Samples for Multi-Omics Approach. Cancers (Basel) 2023; 15:3742. [PMID: 37509403 PMCID: PMC10378006 DOI: 10.3390/cancers15143742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/16/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Biobanks are vital for high-throughput translational research, but the rapid development of novel molecular techniques, especially in omics assays, poses challenges to traditional practices and recommendations. In our study, we used biospecimens from oncological patients in Polish clinics and collaborated with the Indivumed Group. For serum/plasma samples, we monitored hemolysis, controlled RNA extraction, assessed cDNA library quality and quantity, and verified NGS raw data. Tissue samples underwent pathologic evaluation to confirm histology and determine tumor content. Molecular quality control measures included evaluating the RNA integrity number, assessing cDNA library quality and quantity, and analyzing NGS raw data. Our study yielded the creation of distinct workflows for conducting preanalytical quality control of serum/plasma and fresh-frozen tissue samples. These workflows offer customization options to suit the capabilities of different biobanking entities. In order to ensure the appropriateness of biospecimens for advanced research applications, we introduced molecular-based quality control methods that align with the demands of high-throughput assays. The novelty of proposed workflows, rooted in innovative molecular techniques, lies in the integration of these QC methods into a comprehensive schema specifically designed for high-throughput research applications.
Collapse
Affiliation(s)
- Anna Michalska-Falkowska
- Biobank, Medical University of Bialystok, 15-269 Bialystok, Poland
- Indivumed Services, 20251 Hamburg, Germany
| | - Jacek Niklinski
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland
| | | | - Anetta Sulewska
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland
| | - Joanna Kisluk
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland
| | - Radoslaw Charkiewicz
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland
- Center of Experimental Medicine, Medical University of Bialystok, 15-369 Bialystok, Poland
| | - Michal Ciborowski
- Clinical Research Centre, Medical University of Bialystok, 15-276 Bialystok, Poland
| | - Rodryg Ramlau
- Department of Oncology, Poznan University of Medical Sciences, 60-569 Poznan, Poland
| | - Robert Gryczka
- Department of Oncology, Poznan University of Medical Sciences, 60-569 Poznan, Poland
| | - Cezary Piwkowski
- Department of Thoracic Surgery, Poznan University of Medical Sciences, 60-569 Poznan, Poland
| | - Miroslaw Kozlowski
- Department of Thoracic Surgery, Medical University of Bialystok, 15-269 Bialystok, Poland
| | - Borys Miskiewicz
- Department of Thoracic Surgery, Medical University of Bialystok, 15-269 Bialystok, Poland
| | - Przemyslaw Biecek
- Faculty of Mathematics and Information Science, Warsaw University of Technology, 00-662 Warsaw, Poland
| | - Karolina Wnorowska
- Department of Medical Pathomorphology, Medical University of Bialystok, 15-269 Bialystok, Poland
- Department of Paediatrics and Pediatric Neurology, Jedrzej Sniadecki Independent Public Healthcare Centre Regional Hospital, 15-278 Bialystok, Poland
| | - Zofia Dzieciol-Anikiej
- Biobank, Medical University of Bialystok, 15-269 Bialystok, Poland
- Department of Rehabilitation, Medical University of Bialystok, 15-089 Bialystok, Poland
| | - Karine Sargsyan
- International Biobanking and Education, Medical University of Graz, 8036 Graz, Austria
- Cancer Biobank at Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Wojciech Naumnik
- 1st Department of Lung Diseases and Tuberculosis, Medical University of Bialystok, 15-540 Bialystok, Poland
| | - Robert Mroz
- 2nd Department of Lung Diseases and Tuberculosis, Medical University of Bialystok, 15-540 Bialystok, Poland
| | - Joanna Reszec-Gielazyn
- Biobank, Medical University of Bialystok, 15-269 Bialystok, Poland
- Department of Medical Pathomorphology, Medical University of Bialystok, 15-269 Bialystok, Poland
| |
Collapse
|
2
|
Özdemir V, Endrenyi L, Hekim N, Kunej T, Steuten LM, Springer S, Şardaş S, Ergüler E, Bayram M. To Genotype or Phenotype for Drug and Food Safety? Exiting the Technology Echo Chambers. OMICS 2018; 22:525-527. [PMID: 30036157 DOI: 10.1089/omi.2018.0111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Vural Özdemir
- 1 Editor-in-Chief, OMICS: A Journal of Integrative Biology, Mary Ann Liebert, Inc., New Rochelle, New York
| | - Laszlo Endrenyi
- 2 Department of Pharmacology, Faculty of Medicine, University of Toronto , Toronto, Ontario, Canada
| | - Nezih Hekim
- 3 Department of Clinical Biochemistry, School of Medicine, Cumhuriyet University , Sivas, Turkey
| | - Tanja Kunej
- 4 Department of Animal Science, Biotechnical Faculty, University of Ljubljana , Domzale, Slovenia
| | - Lotte M Steuten
- 5 Fred Hutchinson Cancer Research Center , Seattle, Washington
| | - Simon Springer
- 6 Critical Geographies Research Laboratory, Department of Geography, University of Victoria, Victoria, Canada
| | - Semra Şardaş
- 7 Toxicology Unit, Faculty of Pharmacy, İstinye University , İstanbul, Turkey
| | - Erol Ergüler
- 8 Integrative Medicine Clinic , Nişantaşı, İstanbul, Turkey
| | - Mustafa Bayram
- 9 Department of Food Engineering, Faculty of Engineering, Gaziantep University , Gaziantep, Turkey
| |
Collapse
|
3
|
Fang YK, Chien KY, Huang KY, Cheng WH, Ku FM, Lin R, Chen TW, Huang PJ, Chiu CH, Tang P. Responding to a Zoonotic Emergency with Multi-omics Research: Pentatrichomonas hominis Hydrogenosomal Protein Characterization with Use of RNA Sequencing and Proteomics. OMICS 2017; 20:662-669. [PMID: 27828770 DOI: 10.1089/omi.2016.0111] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Pentatrichomonas hominis is an anaerobic flagellated protist that colonizes the large intestine of a number of mammals, including cats, dogs, nonhuman primates, and humans. The wide host range of this organism is alarming and suggests a rising zoonotic emergency. However, knowledge on in-depth biology of this protist is still limited. Similar to the human pathogen, Trichomonas vaginalis, P. hominis possesses hydrogenosomes instead of mitochondria. Studies in T. vaginalis indicated that hydrogenosome is essential for cell survival and associated with numerous pivotal biological functions, including drug resistance. To further decipher the biology of this important organelle, we undertook proteomic research in P. hominis hydrogenosomes. Lacking a decoded P. hominis genome, we utilized an RNA sequencing (RNA-seq) data set generated from P. hominis axenic culture as the reference for proteome analysis. Using this in-house reference data set and mass spectrometry (MS), we identified 442 putative hydrogenosomal proteins. Interestingly, the composition of the P. hominis hydrogenosomal proteins is very similar to that of T. vaginalis, but proteins such as Hmp36, Pam16, Pam18, and Isd11 are absent based on both MS and the RNA-seq. Our data underscore that P. hominis expresses different homologs of multiple gene families from T. vaginalis. To the best of our knowledge, we present here the first hydrogenosome proteome in a protist other than T. vaginalis that offers crucial new scholarship for global health, therapeutics, diagnostics, and veterinary medicine research. In addition, the research strategy used here using RNA sequencing and proteomics might inform future multi-omics research in other understudied organisms without decoded genomes.
Collapse
Affiliation(s)
- Yi-Kai Fang
- 1 Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University , Taoyuan, Taiwan .,2 Molecular Regulation and Bioinformatics Laboratory, Department of Parasitology, Chang Gung University , Taoyuan, Taiwan
| | - Kun-Yi Chien
- 3 Proteomics Core Laboratory, Chang Gung University , Taoyuan, Taiwan
| | - Kuo-Yang Huang
- 2 Molecular Regulation and Bioinformatics Laboratory, Department of Parasitology, Chang Gung University , Taoyuan, Taiwan
| | - Wei-Hung Cheng
- 1 Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University , Taoyuan, Taiwan .,2 Molecular Regulation and Bioinformatics Laboratory, Department of Parasitology, Chang Gung University , Taoyuan, Taiwan
| | - Fu-Mann Ku
- 2 Molecular Regulation and Bioinformatics Laboratory, Department of Parasitology, Chang Gung University , Taoyuan, Taiwan
| | - Rose Lin
- 2 Molecular Regulation and Bioinformatics Laboratory, Department of Parasitology, Chang Gung University , Taoyuan, Taiwan
| | - Ting-Wen Chen
- 4 Bioinformatics Core Laboratory, Chang Gung University , Taoyuan, Taiwan
| | - Po-Jung Huang
- 4 Bioinformatics Core Laboratory, Chang Gung University , Taoyuan, Taiwan
| | - Cheng-Hsun Chiu
- 5 Molecular Infectious Diseases Research Center, Chang Gung Memorial Hospital , Taoyuan, Taiwan
| | - Petrus Tang
- 1 Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University , Taoyuan, Taiwan .,2 Molecular Regulation and Bioinformatics Laboratory, Department of Parasitology, Chang Gung University , Taoyuan, Taiwan .,4 Bioinformatics Core Laboratory, Chang Gung University , Taoyuan, Taiwan .,5 Molecular Infectious Diseases Research Center, Chang Gung Memorial Hospital , Taoyuan, Taiwan
| |
Collapse
|
4
|
Badoud F, Brewer D, Charchoglyan A, Cuthbertson DJ, Mutch DM. Multi-omics Integrative Investigation of Fatty Acid Metabolism in Obese and Lean Subcutaneous Tissue. OMICS 2017; 21:371-379. [PMID: 28618245 DOI: 10.1089/omi.2017.0049] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
White adipose tissue (WAT) plays a central role in whole-body energy homeostasis through storage and release of fatty acids. A deeper understanding of the complex and highly integrated pathways regulating WAT fatty acid metabolism, and how they are altered with obesity, is necessary for diagnostic and therapeutic innovations in nutritional disorders. In this multi-omics study, we investigated the influence of obesity on fatty acid metabolism in human subcutaneous adipose tissue (SAT) using an approach that integrated transcriptomic, peptidomic, and fatty acid analyses. Notably, all analyses were conducted in the same adipose tissue sample from each participant, thus minimizing the chance of spurious results. In a sample of SAT from the periumbilical abdominal region of obese (n = 11, mean body mass index [BMI] = 35.0 ± 1.2 kg/m2) and lean subjects (n = 9, mean BMI = 22.1 ± 0.5 kg/m2), we found that obese SAT tended to have higher relative amounts of specific monounsaturated fatty acids and n-6 polyunsaturated fatty acids, and lower amounts of saturated fatty acids (p < 0.05). These changes were associated with differential regulation of lipogenic and lipolytic pathways in obese SAT. Fatty acid analysis showed changes in estimated fatty acid desaturase and elongase activities between lean and obese SAT (p < 0.05). Biomarkers of lipogenesis (e.g., fatty acid synthase protein) were differentially regulated between lean and obese SAT. These changes were noted in conjunction with increases in extracellular matrix remodeling proteins. Transcriptomic data revealed that the key regulators of lipolysis were reduced in obese SAT. This integrative multi-omics analysis collectively shows that obese SAT has a distinct fatty acid signature compared to lean SAT and the pathways underlying fatty acid metabolism are broadly regulated at the level of gene expression and protein abundance.
Collapse
Affiliation(s)
- Flavia Badoud
- 1 Department of Human Health & Nutritional Sciences, University of Guelph , Guelph, Ontario, Canada
| | - Dyanne Brewer
- 2 Department of Molecular and Cellular Biology, University of Guelph , Guelph, Ontario, Canada
| | - Armen Charchoglyan
- 2 Department of Molecular and Cellular Biology, University of Guelph , Guelph, Ontario, Canada
| | | | - David M Mutch
- 1 Department of Human Health & Nutritional Sciences, University of Guelph , Guelph, Ontario, Canada
| |
Collapse
|