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Lin CY, Song X, Ke Y, Raha A, Wu Y, Wasi M, Wang L, Geng F, You L. Yoda1 Enhanced Low-Magnitude High-Frequency Vibration on Osteocytes in Regulation of MDA-MB-231 Breast Cancer Cell Migration. Cancers (Basel) 2022; 14:3395. [PMID: 35884459 PMCID: PMC9324638 DOI: 10.3390/cancers14143395] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/07/2022] [Accepted: 07/07/2022] [Indexed: 02/05/2023] Open
Abstract
Low-magnitude (≤1 g) high-frequency (≥30 Hz) (LMHF) vibration has been shown to enhance bone mineral density. However, its regulation in breast cancer bone metastasis remains controversial for breast cancer patients and elder populations. Yoda1, an activator of the mechanosensitive Piezo1 channel, could potentially intensify the effect of LMHF vibration by enhancing the mechanoresponse of osteocytes, the major mechanosensory bone cells with high expression of Piezo1. In this study, we treated osteocytes with mono- (Yoda1 only or vibration only) or combined treatment (Yoda1 and LMHF vibration) and examined the further regulation of osteoclasts and breast cancer cells through the conditioned medium. Moreover, we studied the effects of combined treatment on breast cancer cells in regulation of osteocytes. Combined treatment on osteocytes showed beneficial effects, including increasing the nuclear translocation of Yes-associated protein (YAP) in osteocytes (488.0%, p < 0.0001), suppressing osteoclastogenesis (34.3%, p = 0.004), and further reducing migration of MDA-MB-231 (15.1%, p = 0.02) but not Py8119 breast cancer cells (4.2%, p = 0.66). Finally, MDA-MB-231 breast cancer cells subjected to the combined treatment decreased the percentage of apoptotic osteocytes (34.5%, p = 0.04) but did not affect the intracellular calcium influx. This study showed the potential of stimulating Piezo1 in enhancing the mechanoresponse of osteocytes to LMHF vibration and further suppressing breast cancer migration via osteoclasts.
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Affiliation(s)
- Chun-Yu Lin
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada; (C.-Y.L.); (Y.K.)
| | - Xin Song
- Mechanical and Industrial Engineering, University of Toronto, Toronto, ON M5S 3G8, Canada;
| | - Yaji Ke
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada; (C.-Y.L.); (Y.K.)
| | - Arjun Raha
- W Booth School of Engineering Practice and Technology, McMaster University, Hamilton, ON L8S 4L7, Canada; (A.R.); (Y.W.); (F.G.)
| | - Yuning Wu
- W Booth School of Engineering Practice and Technology, McMaster University, Hamilton, ON L8S 4L7, Canada; (A.R.); (Y.W.); (F.G.)
| | - Murtaza Wasi
- Department of Mechanical Engineering, University of Delaware, Newark, DE 19716, USA; (M.W.); (L.W.)
| | - Liyun Wang
- Department of Mechanical Engineering, University of Delaware, Newark, DE 19716, USA; (M.W.); (L.W.)
| | - Fei Geng
- W Booth School of Engineering Practice and Technology, McMaster University, Hamilton, ON L8S 4L7, Canada; (A.R.); (Y.W.); (F.G.)
| | - Lidan You
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada; (C.-Y.L.); (Y.K.)
- Mechanical and Industrial Engineering, University of Toronto, Toronto, ON M5S 3G8, Canada;
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Jaiswal KS, Khanna S, Ghosh A, Padhan P, Raghav SK, Gupta B. Differential mitochondrial genome in patients with Rheumatoid Arthritis. Autoimmunity 2020; 54:1-12. [PMID: 33191792 DOI: 10.1080/08916934.2020.1846182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
BACKGROUND Mitochondria play an important role in cell survival, function and lineage differentiation. Changes in mitochondrial DNA (mtDNA) may control mitochondrial functions and thus may impart an alternative cellular state thereby leading to a disease condition in the body. Rheumatoid arthritis (RA) is a chronic inflammatory autoimmune disease wherein immune cells become self-reactive causing joint inflammation, swelling and pain in patients. The changes in mtDNA may alter cellular functions thereby directing the immune cells towards an inflammatory phenotype in RA. Therefore, it becomes pertinent to identify changes in mtDNA sequence in immune cells of RA patients to understand the pathogenesis and progression of RA. METHODS mtDNA from peripheral blood mono-nuclear cells (PBMCs) of 23 RA patients and 17 healthy controls (HCs) were sequenced using next-generation sequencing (NGS). Further, single nucleotide polymorphisms (SNPs) and other variable changes in mtDNA hypervariable and coding regions, amino acid changes with a putative impact on disease, levels of heteroplasmy, copy number variations and haplogroup analysis in RA patients and HCs were analysed and compared to identify any association of mtDNA changes and RA disease. RESULTS A total of 382 single nucleotide mtDNA variants were observed, 91 (23.82%) were present in hypervariable region and 291 (76.18%) in coding region of patients and HC. The variant 513 GCA > ACA, with G present in HVR-III, known to control the mitochondrial translation function, was significantly present in RA patients. The CYTB gene had larger number of SNPs in HC samples while RNR2 was more variable in RA patients. A non-synonymous heteroplasmy in ND1 gene was found at a single nucleotide position 3533 in an increased number of RA patients as compared to the controls. A significant increase in mtDNA duplication and a higher frequency of the haplogroup U was also characteristic of RA. Also, the presence of SNPs in mitochondrial tRNA genes at two positions 12308 A > G and 15924 A > G were found to be pathogenic. CONCLUSION We herein observed an altered mtDNA sequence in immune cells of RA patients and thus a possible role of mitochondrial genome in the development of RA. The observed nucleotide changes in mtDNA control region, RNR2 gene, increased heteroplasmy and mtDNA duplication in RA patients may alter sites for transcription factor binding thereby influencing mtDNA gene expression, as well as copy numbers thereby affecting the mitochondrial proteins and their functions. These changes in mtDNA could be one of the probable reasons among many leading to the progression of RA.
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Affiliation(s)
- Kumar Sagar Jaiswal
- Disease Biology Laboratory, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India
| | - Shweta Khanna
- Disease Biology Laboratory, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India
| | - Arup Ghosh
- Laboratory of Immuno-Genomics and Systems Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Prasanta Padhan
- Department of Rheumatology, Kalinga Institute of Medical Sciences, Bhubaneswar, India
| | - Sunil Kumar Raghav
- Laboratory of Immuno-Genomics and Systems Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Bhawna Gupta
- Disease Biology Laboratory, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India
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Nguyen H, LaFramboise T. Complexities and pitfalls in analyzing and interpreting mitochondrial DNA content in human cancer. J Genet Genomics 2020; 47:349-359. [PMID: 33004308 DOI: 10.1016/j.jgg.2020.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 04/01/2020] [Accepted: 04/20/2020] [Indexed: 11/29/2022]
Abstract
Mutations in the human mitochondrial genome have been observed in all types of human cancer, indicating that mutations might contribute to tumorigenesis, metastasis, recurrence, or drug response. This possibility is appealing because of the known shift from oxidative metabolism to glycolysis, known as the Warburg effect, that occurs in malignancy. Mitochondrial DNA (mtDNA) mutations could either be maternally inherited and predispose to cancer (germ line mutations) or occur sporadically in the mtDNA of specific tissues (tissue- or tumor-specific somatic mutations) and contribute to the tumor initiation and progression process. High-throughput sequencing technologies now enable comprehensive detection of mtDNA variation in tissues and bodily fluids, with the potential to be used as an early detection tool that may impact the treatment of cancer. Here, we discuss insights into the roles of mtDNA mutations in carcinogenesis, highlighting the complexities involved in the analysis and interpretation of mitochondrial genomic content, technical challenges in studying their contribution to pathogenesis, and the value of mtDNA mutations in developing early detection, diagnosis, prognosis, and therapeutic strategies for cancer.
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Affiliation(s)
- Hieu Nguyen
- Vinmec Research Institute of Stem Cell and Gene Technology (VRSIG), 458 Minh Khai, Vinh Tuy, Hai Ba Trung, Hanoi, Viet Nam; Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Thomas LaFramboise
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA.
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Weerts MJA, Timmermans EC, Vossen RHAM, van Strijp D, Van den Hout-van Vroonhoven MCGN, van IJcken WFJ, van der Zaag PJ, Anvar SY, Sleijfer S, Martens JWM. Sensitive detection of mitochondrial DNA variants for analysis of mitochondrial DNA-enriched extracts from frozen tumor tissue. Sci Rep 2018; 8:2261. [PMID: 29396409 PMCID: PMC5797170 DOI: 10.1038/s41598-018-20623-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 01/22/2018] [Indexed: 11/25/2022] Open
Abstract
Large variation exists in mitochondrial DNA (mtDNA) not only between but also within individuals. Also in human cancer, tumor-specific mtDNA variation exists. In this work, we describe the comparison of four methods to extract mtDNA as pure as possible from frozen tumor tissue. Also, three state-of-the-art methods for sensitive detection of mtDNA variants were evaluated. The main aim was to develop a procedure to detect low-frequent single-nucleotide mtDNA-specific variants in frozen tumor tissue. We show that of the methods evaluated, DNA extracted from cytosol fractions following exonuclease treatment results in highest mtDNA yield and purity from frozen tumor tissue (270-fold mtDNA enrichment). Next, we demonstrate the sensitivity of detection of low-frequent single-nucleotide mtDNA variants (≤1% allele frequency) in breast cancer cell lines MDA-MB-231 and MCF-7 by single-molecule real-time (SMRT) sequencing, UltraSEEK chemistry based mass spectrometry, and digital PCR. We also show de novo detection and allelic phasing of variants by SMRT sequencing. We conclude that our sensitive procedure to detect low-frequent single-nucleotide mtDNA variants from frozen tumor tissue is based on extraction of DNA from cytosol fractions followed by exonuclease treatment to obtain high mtDNA purity, and subsequent SMRT sequencing for (de novo) detection and allelic phasing of variants.
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Affiliation(s)
- M J A Weerts
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Rotterdam, The Netherlands.
| | - E C Timmermans
- Philips Research Laboratories, High Tech Campus 11, 5656 AE, Eindhoven, The Netherlands
| | - R H A M Vossen
- Leiden Genome Technology Center (LGTC), Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - D van Strijp
- Philips Research Laboratories, High Tech Campus 11, 5656 AE, Eindhoven, The Netherlands
| | | | | | - P J van der Zaag
- Philips Research Laboratories, High Tech Campus 11, 5656 AE, Eindhoven, The Netherlands
| | - S Y Anvar
- Leiden Genome Technology Center (LGTC), Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.,Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.,Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, The Netherlands
| | - S Sleijfer
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - J W M Martens
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
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Ahmad S, Ghosh A, Nair DL, Seshadri M. Simultaneous extraction of nuclear and mitochondrial DNA from human blood. Genes Genet Syst 2008; 82:429-32. [PMID: 17991998 DOI: 10.1266/ggs.82.429] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
A method of simultaneous isolation of nuclear DNA (nDNA) and mitochondrial DNA (mtDNA) from human blood has been proposed by improvising Lahiri's method of isolation of nuclear DNA. The approach presented here provides selectively enriched fractions and eliminates the need for two different methods or separate reagent sets for the extraction of nDNA and mtDNA. It employs an initial nuclear/ cytoplasm partitioning, followed by the similar procedural steps for the two fractions separately. It gives good quality and quantity of the nDNA as well as the mtDNA, suitable for processes like PCR amplification and sequencing and may prove to be useful for people studying population genetics and evolution using molecular markers maximizing the available resources, especially in cases where a large database needs to be generated from limited amount of blood sample. From 3 ml of blood, the yields of mtDNA salvaged from the supernatant were sufficient to set approximately 4x10(5) reactions (starting with 250 fg DNA per reactions) of mtDNA loci which otherwise would have been discarded as per original Lahiri's procedure. The quality of mtDNA from the mitochondrial fraction was suitable for all major downstream processes as confirmed by locus specific PCR amplifications and sequencing. Through this procedure, the wastage of nDNA can be avoided when mtDNA loci is studied.
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Affiliation(s)
- Shazia Ahmad
- Low Level Radiation Studies Section, Radiation Biology and Health Science Division, Bio-Medical Group, Bhabha Atomic Research Center, Mumbai, India.
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6
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Choi YJ, Yim DS, Cho JS, Cho BD, Na KJ, Gi Baik M. Analysis of restriction fragment length polymorphism in the bovine growth hormone gene related to growth performance and carcass quality of Korean Native Cattle. Meat Sci 1997; 45:405-10. [DOI: 10.1016/s0309-1740(96)00085-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/1996] [Revised: 04/28/1996] [Accepted: 06/29/1996] [Indexed: 11/28/2022]
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Bradley DG, MacHugh DE, Cunningham P, Loftus RT. Mitochondrial diversity and the origins of African and European cattle. Proc Natl Acad Sci U S A 1996; 93:5131-5. [PMID: 8643540 PMCID: PMC39419 DOI: 10.1073/pnas.93.10.5131] [Citation(s) in RCA: 298] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The nature of domestic cattle origins in Africa are unclear as archaeological data are relatively sparse. The earliest domesticates were humpless, or Bos taurus, in morphology and may have shared a common origin with the ancestors of European cattle in the Near East. Alternatively, local strains of the wild ox, the aurochs, may have been adopted by peoples in either continent either before or after cultural influence from the Levant. This study examines mitochondrial DNA displacement loop sequence variation in 90 extant bovines drawn from Africa, Europe, and India. Phylogeny estimation and analysis of molecular variance verify that sequences cluster significantly into continental groups. The Indian Bos indicus samples are most markedly distinct from the others, which is indicative of a B. taurus nature for both European and African ancestors. When a calibration of sequence divergence is performed using comparisons with bison sequences and an estimate of 1 Myr since the Bison/Bos Leptobos common ancestor, estimates of 117-275,000 B.P. and 22-26,000 B.P. are obtained for the separation between Indians and others and between African and European ancestors, respectively. As cattle domestication is thought to have occurred approximately 10,000 B.P., these estimates suggest the domestication of genetically discrete aurochsen strains as the origins of each continental population. Additionally, patterns of variation that are indicative of population expansions (probably associated with the domestication process) are discernible in Africa and Europe. Notably, the genetic signatures of these expansions are clearly younger than the corresponding signature of African/European divergence.
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Affiliation(s)
- D G Bradley
- Department of Genetics, Trinity College, Dublin, Ireland
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Boettcher PJ, Freeman AE, Johnston SD, Smith RK, Beitz DC, McDaniel BT. Relationships between polymorphism for mitochondrial deoxyribonucleic acid and yield traits of Holstein cows. J Dairy Sci 1996; 79:647-54. [PMID: 8744230 DOI: 10.3168/jds.s0022-0302(96)76410-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Two independent data files from the breeding herd of Iowa State University and six North Carolina herds were used to examine relationships between yield traits and mtDNA polymorphism. Maternal lineages were established by tracing ancestry of cows to founder females in the herd book of the Holstein Association. Data from Iowa State University were 1476 records from 602 cows from 29 maternal lineages. The nucleotides of mtDNA encoding rRNA were sequenced. Eleven sites of polymorphism were found. An animal model for gene substitution was used to examine the relationship between sequence differences and yield traits. Traits analyzed were mature equivalent yield of milk, fat, SNF, and milk energy as well as concentrations of fat, SNF, and milk energy. Effects of sequence differences were significant for most traits. Sequence information from the D-loop was available for 12 lineages from North Carolina. The effect of polymorphism at 4 sites was examined using 1472 records from 668 cows. Traits measured were the same, except that protein replaced SNF. No significant relationships existed between any of the traits and D-loop polymorphism, but results suggested that an association might exist between polymorphism and concentrations of milk yield, fat percentage, and energy. Whenever a significant relationship was detected, the effect of mutation (rare genotype) was detrimental.
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Affiliation(s)
- P J Boettcher
- Department of Animal Science, Iowa State University, Ames 50011, USA
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Pegoraro L, Yang Z, Samaké S, Meirelles FV, Bordingnon V, Moquin LC, Smith LC. Sequence comparison of mitochondrial tRNA genes and origin of light strand replication in Bos taurus and Nellore (Bos indicus) breeds. Anim Genet 1996; 27:91-4. [PMID: 8856897 DOI: 10.1111/j.1365-2052.1996.tb00473.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Although the complete bovine mitochondrial DNA molecule has been previously sequenced and sequence comparisons of the mitochondrial displacement loop have been performed, detailed sequence information is limited on coding regions of mitochondrial DNA within and among breeds of Bos taurus and Bos indicus. This study analysed polymorphism of the mitochondrial DNA transfer RNA genes for tryptophan, alanine, asparagine, cysteine, tyrosine and the origin of light strand replication among Ayrshire, Canadian, Belgium Blue, Brown Swiss, Hereford, Jersey, Limousine, Piedmontaise, Red Angus, Simmental (Bos taurus) and a Nellore (Bos indicus). Nucleotide sequence analysis of a 420-bp fragment of mitochondrial DNA comprising the five transfer RNA genes showed 100% homology among single individuals of the Bos taurus breeds. The Nellore breed showed guanine to adenine substitutions in the DHU arm of asparagine tRNA and in the origin of light-strand replication. This equates to a 0.5% sequence difference between the Nellore and Bos taurus breeds and may reflect an independent evolutionary origin of the species.
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Affiliation(s)
- L Pegoraro
- Centre de recherche en reproduction animale (CRRA), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Québec, Canada
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Loftus RT, MacHugh DE, Ngere LO, Balain DS, Badi AM, Bradley DG, Cunningham EP. Mitochondrial genetic variation in European, African and Indian cattle populations. Anim Genet 1994; 25:265-71. [PMID: 7985843 DOI: 10.1111/j.1365-2052.1994.tb00203.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Mitochondrial DNA from representative animals of 13 different cattle breeds was assayed for restriction fragment length polymorphisms (RFLP) to determine phylogenetic relationships and levels of variation among breeds; 16 different mitotypes were found, described by 20 polymorphisms. Within these 16 mitotypes two major lineages were apparent: an Afro-European and an Asian type. These were found to differ at over 2.3% of sites surveyed. None of the mitotypes found in the Asian lineage was detectable in the Afro-European lineage and vice versa. Within each of the major mitotypes there were no further significant differences within or among breeds. Using rates of mitochondrial evolution estimated from other species, the two lineages were estimated to have diverged between 575,000 and 1,150,000 years ago; well outside the 10,000 years bp timeframe postulated by a single domestication hypothesis. The results presented are concordant with those generated in other studies and provide strong evidence for an independent domestication of Asian Bos indicus. Furthermore, the grouping of all African indicine populations within the clade containing all Bos taurus lineages points to the hybrid origins of the humped cattle of that continent.
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Affiliation(s)
- R T Loftus
- Department of Genetics, Trinity College, Dublin, Ireland
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Loftus RT, MacHugh DE, Bradley DG, Sharp PM, Cunningham P. Evidence for two independent domestications of cattle. Proc Natl Acad Sci U S A 1994; 91:2757-61. [PMID: 8146187 PMCID: PMC43449 DOI: 10.1073/pnas.91.7.2757] [Citation(s) in RCA: 431] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The origin and taxonomic status of domesticated cattle are controversial. Zebu and taurine breeds are differentiated primarily by the presence or absence of a hump and have been recognized as separate species (Bos indicus and Bos taurus). However, the most widely held view is that both types of cattle derive from a single domestication event 8000-10,000 years ago. We have examined mtDNA sequences from representatives of six European (taurine) breeds, three Indian (zebu) breeds, and four African (three zebu, one taurine) breeds. Similar levels of average sequence divergence were observed among animals within each of the major continental groups: 0.41% (European), 0.38% (African), and 0.42% (Indian). However, the sequences fell into two very distinct geographic lineages that do not correspond with the taurine-zebu dichotomy: all European and African breeds are in one lineage, and all Indian breeds are in the other. There was little indication of breed clustering within either lineage. Application of a molecular clock suggests that the two major mtDNA clades diverged at least 200,000, and possibly as much as 1 million, years ago. This relatively large divergence is interpreted most simply as evidence for two separate domestication events, presumably of different subspecies of the aurochs, Bos primigenius. The clustering of all African zebu mtDNA sequences within the taurine lineage is attributed to ancestral crossbreeding with the earlier B. taurus inhabitants of the continent.
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Affiliation(s)
- R T Loftus
- Department of Genetics, Trinity College, Dublin, Ireland
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