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Toxicologic Pathology Jun 2007The process of programmed cell death, or apoptosis, is generally characterized by distinct morphological characteristics and energy-dependent biochemical mechanisms.... (Review)
Review
The process of programmed cell death, or apoptosis, is generally characterized by distinct morphological characteristics and energy-dependent biochemical mechanisms. Apoptosis is considered a vital component of various processes including normal cell turnover, proper development and functioning of the immune system, hormone-dependent atrophy, embryonic development and chemical-induced cell death. Inappropriate apoptosis (either too little or too much) is a factor in many human conditions including neurodegenerative diseases, ischemic damage, autoimmune disorders and many types of cancer. The ability to modulate the life or death of a cell is recognized for its immense therapeutic potential. Therefore, research continues to focus on the elucidation and analysis of the cell cycle machinery and signaling pathways that control cell cycle arrest and apoptosis. To that end, the field of apoptosis research has been moving forward at an alarmingly rapid rate. Although many of the key apoptotic proteins have been identified, the molecular mechanisms of action or inaction of these proteins remain to be elucidated. The goal of this review is to provide a general overview of current knowledge on the process of apoptosis including morphology, biochemistry, the role of apoptosis in health and disease, detection methods, as well as a discussion of potential alternative forms of apoptosis.
Topics: Animals; Apoptosis; DNA Fragmentation; Humans; Necrosis
PubMed: 17562483
DOI: 10.1080/01926230701320337 -
Andrologia Mar 2021We herein summarise the evidence concerning the impact of sperm DNA fragmentation in various clinical infertility scenarios and the advances on sperm DNA fragmentation... (Review)
Review
We herein summarise the evidence concerning the impact of sperm DNA fragmentation in various clinical infertility scenarios and the advances on sperm DNA fragmentation tests. The collected evidence was used to formulate 41 recommendations. Of these, 13 recommendations concern technical aspects of sperm DNA fragmentation testing, including pre-analytical information, clinical thresholds and interpretation of results. The remaining 28 recommendations relate to indications for sperm DNA fragmentation testing and clinical management. Clinical scenarios like varicocele, unexplained infertility, idiopathic infertility, recurrent pregnancy loss, intrauterine insemination, in vitro fertilisation/intracytoplasmic sperm injection, fertility counselling for men with infertility risk factors and sperm cryopreservation have been contemplated. The bulk evidence supporting the recommendations has increased in recent years, but it is still of moderate to low quality. This guideline provides clinicians with advice on best practices in sperm DNA fragmentation testing. Also, recommendations are provided on possible management strategies to overcome infertility related to sperm DNA fragmentation, based on the best available evidence. Lastly, we identified gaps in knowledge and opportunities for research and elaborated a list of recommendations to stimulate further investigation.
Topics: DNA Fragmentation; Female; Humans; Infertility, Male; Male; Pregnancy; Sperm Injections, Intracytoplasmic; Spermatozoa; Varicocele
PubMed: 33108829
DOI: 10.1111/and.13874 -
Bioinformatics (Oxford, England) Aug 2021Circulating cell-free DNA (cfDNA) is a promising biomarker for the diagnosis and prognosis of many diseases, including cancer. The genome-wide non-random fragmentation...
SUMMARY
Circulating cell-free DNA (cfDNA) is a promising biomarker for the diagnosis and prognosis of many diseases, including cancer. The genome-wide non-random fragmentation patterns of cfDNA are associated with the nucleosomal protection, epigenetic environment and gene expression in the cell types that contributed to cfDNA. However, current progress on the development of computational methods and understanding of molecular mechanisms behind cfDNA fragmentation patterns is significantly limited by the controlled-access of cfDNA whole-genome sequencing (WGS) dataset. Here, we present FinaleDB (FragmentatIoN AnaLysis of cEll-free DNA DataBase), a comprehensive database to host thousands of uniformly processed and curated de-identified cfDNA WGS datasets across different pathological conditions. Furthermore, FinaleDB comes with a fragmentation genome browser, from which users can seamlessly integrate thousands of other omics data in different cell types to experience a comprehensive view of both gene-regulatory landscape and cfDNA fragmentation patterns.
AVAILABILITY AND IMPLEMENTATION
FinaleDB service: http://finaledb.research.cchmc.org/. FinaleDB source code: https://github.com/epifluidlab/finaledb_portal, https://github.com/epifluidlab/finaledb_workflow.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
Topics: Cell-Free Nucleic Acids; DNA Fragmentation; Genome; Software; Whole Genome Sequencing
PubMed: 33258919
DOI: 10.1093/bioinformatics/btaa999 -
BMC Biology Nov 2023Circulating cell-free DNA (cfDNA) is a pool of short DNA fragments mainly released from apoptotic hematopoietic cells. Nevertheless, the precise physiological process...
BACKGROUND
Circulating cell-free DNA (cfDNA) is a pool of short DNA fragments mainly released from apoptotic hematopoietic cells. Nevertheless, the precise physiological process governing the DNA fragmentation and molecular profile of cfDNA remains obscure. To dissect the DNA fragmentation process, we use a human leukemia cell line HL60 undergoing apoptosis to analyze the size distribution of DNA fragments by shallow whole-genome sequencing (sWGS). Meanwhile, we also scrutinize the size profile of plasma cfDNA in 901 healthy human subjects and 38 dogs, as well as 438 patients with six common cancer types by sWGS.
RESULTS
Distinct size distribution profiles were observed in the HL60 cell pellet and supernatant, suggesting fragmentation is a stepwise process. Meanwhile, C-end preference was seen in both intracellular and extracellular cfDNA fragments. Moreover, the cfDNA profiles are characteristic and conserved across mammals. Compared with healthy subjects, distinct cfDNA profiles with a higher proportion of short fragments and lower C-end preference were found in cancer patients.
CONCLUSIONS
Our study provides new insight into fragmentomics of circulating cfDNA processing, which will be useful for early diagnosis of cancer and surveillance during cancer progression.
Topics: Humans; Animals; Dogs; DNA Fragmentation; Cell-Free Nucleic Acids; Neoplasms; DNA; Apoptosis; Mammals
PubMed: 37953260
DOI: 10.1186/s12915-023-01752-6 -
Fertility and Sterility Aug 2020
Topics: Chromatin; DNA; DNA Fragmentation; Fertility Clinics; Humans; Male; Paternal Age; Spermatozoa
PubMed: 32741463
DOI: 10.1016/j.fertnstert.2020.05.011 -
Genomics Nov 2022Cell-free DNA (cfDNA), as a non-invasive approach, has been introduced in a wide range of applications, including cancer diagnosis/ monitoring, prenatal testing, and...
Cell-free DNA (cfDNA), as a non-invasive approach, has been introduced in a wide range of applications, including cancer diagnosis/ monitoring, prenatal testing, and transplantation monitoring. Yet, studies of cfDNA fragmentomics in physiological conditions are lacking. In this study, we aim to explore the correlation of fragmentation patterns of cfDNA with blood biochemical and hematological parameters in healthy individuals. We addressed the impact of physiological variables and abnormal blood biochemical and hematological parameters on cfDNA fragment size distribution. We also figured and validated that hematological inflammation markers, including leukocyte, lymphocyte, neutrophil, and platelet distribution width as well as aspartate transaminase levels were significantly correlated with the genome-wide cfDNA fragmentation pattern. Our findings suggest that cfDNA fragmentation profiles were associated with physiological parameters related to cardiovascular risk factors, inflammatory response and hepatocyte injury, which may provide insights for further research on the potential role of cfDNA fragmentation in diagnosis and monitor of several disease.
Topics: Humans; Cell-Free Nucleic Acids; DNA Fragmentation
PubMed: 36257481
DOI: 10.1016/j.ygeno.2022.110504 -
Reproduction & Fertility Jul 2021Sperm DNA fragmentation (SDF) and sperm morphological defects can negatively affect ART outcomes. Consequently, there is a need for additional semen processing technique...
UNLABELLED
Sperm DNA fragmentation (SDF) and sperm morphological defects can negatively affect ART outcomes. Consequently, there is a need for additional semen processing technique that accounts for sperm DNA status and morphology prior to ICSI. The objective was to evaluate the efficacy of an additional zona pellucida adhesion-based sperm selection for obtaining sperm populations with a high percentage of normal morphology and DNA integrity as compared to native semen and routine swim-up preparation. Semen samples from 78 normozoospermic men were subjected to swim up and placed in petri dishes coated with 48 acid-solubilized zonae pellucidae. Sperm DNA fragmentation and morphology were assessed in the native semen, the swim-up samples, and the zona-adhered spermatozoa from each patient. The mean sperm DNA fragmentation of the zona-selected spermatozoa (3.5 ± 0.7%) was significantly lower than the swim-up samples (15.3 ± 5.2%) ( < 0.001) and native semen (24.9 ± 7.1%) ( < 0.001). All of the samples had lower levels of DNA damage after additional selection by zona pellucida adhesion. Significantly higher percentage of sperm with normal morphology was observed after zona-adhesion selection (11.4 ± 3.9%) when compared to the swim-up samples (8.9 ± 4.3%) ( < 0.001) or the native semen (5.3 ± 3.2%) ( < 0.001). In 94% of the samples, the percentage of spermatozoa with normal morphology increased after the additional zona selection. This study demonstrates that sperm selection by additional zona-adhesion technique yields a significantly higher percentage of spermatozoa with normal morphology as well as a significantly decreased level of DNA fragmentation when compared to the native semen and the swim-up-only prepared samples.
LAY SUMMARY
High level of DNA folding known as sperm DNA fragmentation (SDF) inside each sperm and defects in the shape, size, and structure of the sperm can negatively affect assisted reproduction treatment (ART) outcomes. Consequently, there is a need for additional semen processing techniques that account for sperm quality prior to ART. Our team designed a simple technique using proteins from the coat around the egg (zona pellucida) to enhance sperm selection procedures based on natural sperm-egg interactions. Using this technique in combination with the most common techniques used in ART yields a significantly higher percentage of sperm with normal shape, size, and structure and a decreased level of DNA fragmentation. This sperm zona-selection technique would be beneficial if introduced in the ART practice to yield sperm with higher fertilization potential.
Topics: DNA Fragmentation; Humans; Male; Semen; Sperm-Ovum Interactions; Spermatozoa; Zona Pellucida
PubMed: 35118392
DOI: 10.1530/RAF-21-0041 -
Asian Journal of Andrology 2022The renin angiotensin system (RAS) appears to influence male fertility at multiple levels. In this work, we analyzed the relationship between the RAS and DNA integrity....
The renin angiotensin system (RAS) appears to influence male fertility at multiple levels. In this work, we analyzed the relationship between the RAS and DNA integrity. Fifty male volunteers were divided into two groups (25 each): control (DNA fragmentation ≤20%) and pathological (DNA fragmentation >20%) cases. Activities of five peptidases controlling RAS were measured fluorometrically: prolyl endopeptidase (which converts angiotensin [A] I and A II to A 1-7), neutral endopeptidase (NEP/CD10: A I to A 1-7), aminopeptidase N (APN/CD13: A III to A IV), aminopeptidase A (A II to A III) and aminopeptidase B (A III to A IV). Angiotensin-converting enzyme (A I to A II), APN/CD13 and NEP/CD10 were also assessed by semiquantitative cytometry and quantitative flow cytometry assays, as were the receptors of all RAS components: A II receptor type 1 (AT1R), A II receptor type 2 (AT2R), A IV receptor (AT4R or insulin-regulated aminopeptidase [IRAP]), (pro)renin receptor (PRR) and A 1-7 receptor or Mas receptor (MasR) None of the enzymes that regulate levels of RAS components, except for APN/CD13 (decrease in fragmented cells), showed significant differences between both groups. Micrographs of RAS receptors revealed no significant differences in immunolabeling patterns between normozoospermic and fragmented cells. Labeling of AT1R (94.3% normozoospermic vs 84.1% fragmented), AT4R (96.2% vs 95.3%) and MasR (97.4% vs 87.2%) was similar between the groups. AT2R (87.4% normozoospermic vs 63.1% fragmented) and PRR (96.4% vs 48.2%) were higher in non-fragmented spermatozoa. These findings suggest that fragmented DNA spermatozoa have a lower capacity to respond to bioactive RAS peptides.
Topics: Angiotensins; DNA Fragmentation; Humans; Insulin; Male; Renin-Angiotensin System; Spermatozoa
PubMed: 34494558
DOI: 10.4103/aja202150 -
Fertility and Sterility Dec 2021
Topics: DNA Fragmentation; Humans; Infertility, Male; Male; Spermatozoa
PubMed: 34743912
DOI: 10.1016/j.fertnstert.2021.09.029 -
JBRA Assisted Reproduction Oct 2021This study aimed to assess the effects of sperm DNA fragmentation in parents belonging to different age groups. The couples included in the study comprised...
OBJECTIVE
This study aimed to assess the effects of sperm DNA fragmentation in parents belonging to different age groups. The couples included in the study comprised normozoospermic men and infertile women undergoing conventional IVF.
METHODS
The results obtained from 163 conventional IVF cycles were analyzed retrospectively. The couples enrolled in the study included women aged between 30 and 37 years. Sperm DNA fragmentation was studied using the TUNEL assay. The patients were split into four groups based on male age and sperm DNA fragmentation, as follows: Group 1: ≤39 years and TUNEL assay ≤20%; Group 2: ≤39 years and TUNEL assay >20%; Group 3: ≥40 years and TUNEL assay ≤20%; and Group 4: ≥40 years and TUNEL assay >20%.
RESULTS
No significant differences were found in semen parameters or fertilization rates between groups. Groups with <20% sperm DNA fragmentation showed significant differences in other parameters, including higher blastocyst formation rate (Group 1: 63% and Group 3: 60% vs. Group 2: 43% and Group 4: 41%, p<0.05) and higher expanded blastocyst formation rate (Group 1: 42% and Group 3: 40% vs. Group 2: 21% and Group 4: 18%, p<0.05). Miscarriage rate was significantly higher in Group 4 (42% and 46% vs. 5%, 25% and 5% in Groups 1, 2 and 3, respectively, p<0.05).
CONCLUSIONS
Our results showed lower blastocyst formation rates from IVF when males had high levels of sperm DNA fragmentation. Higher miscarriage rates were also observed in couples with males aged 40+ years. These results reinforce the need to inform couples with male partners aged 40+ years about the potential risks inherent to fertility treatment.
Topics: Adult; DNA Fragmentation; Female; Fertilization in Vitro; Humans; Infertility, Female; Male; Pregnancy; Pregnancy Rate; Retrospective Studies; Sperm Injections, Intracytoplasmic; Spermatozoa
PubMed: 34061484
DOI: 10.5935/1518-0557.20210018