1
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Yang W, Rubin JB. Treating sex and gender differences as a continuous variable can improve precision cancer treatments. Biol Sex Differ 2024; 15:35. [PMID: 38622740 PMCID: PMC11017567 DOI: 10.1186/s13293-024-00607-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 03/21/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND The significant sex and gender differences that exist in cancer mechanisms, incidence, and survival, have yet to impact clinical practice. One barrier to translation is that cancer phenotypes cannot be segregated into distinct male versus female categories. Instead, within this convenient but contrived dichotomy, male and female cancer phenotypes are highly overlapping and vary between female- and male- skewed extremes. Thus, sex and gender-specific treatments are unrealistic, and our translational goal should be adaptation of treatment to the variable effects of sex and gender on targetable pathways. METHODS To overcome this obstacle, we profiled the similarities in 8370 transcriptomes of 26 different adult and 4 different pediatric cancer types. We calculated the posterior probabilities of predicting patient sex and gender based on the observed sexes of similar samples in this map of transcriptome similarity. RESULTS Transcriptomic index (TI) values were derived from posterior probabilities and allowed us to identify poles with local enrichments for male or female transcriptomes. TI supported deconvolution of transcriptomes into measures of patient-specific activity in sex and gender-biased, targetable pathways. It identified sex and gender-skewed extremes in mechanistic phenotypes like cell cycle signaling and immunity, and precisely positioned each patient's whole transcriptome on an axis of continuously varying sex and gender phenotypes. CONCLUSIONS Cancer type, patient sex and gender, and TI value provides a novel and patient- specific mechanistic identifier that can be used for realistic sex and gender-adaptations of precision cancer treatment planning.
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Affiliation(s)
- Wei Yang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Joshua B Rubin
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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2
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Bramwell LR, Frankum R, Harries LW. Repurposing Drugs for Senotherapeutic Effect: Potential Senomorphic Effects of Female Synthetic Hormones. Cells 2024; 13:517. [PMID: 38534362 DOI: 10.3390/cells13060517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/26/2024] [Accepted: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
Repurposing previously approved drugs may fast track the route to the clinic for potential senotherapeutics and improves the inefficiency of the clinical drug development pipeline. We performed a repurposing screen of 240 clinically approved molecules in human primary dermal fibroblasts for their effects on CDKN2A expression. Molecules demonstrating effects on CDKN2A expression underwent secondary screening for senescence-associated beta galactosidase (SAB) activity, based on effect size, direction, and/or molecule identity. Selected molecules then underwent a more detailed assessment of senescence phenotypes including proliferation, apoptosis, DNA damage, senescence-associated secretory phenotype (SASP) expression, and regulators of alternative splicing. A selection of the molecules demonstrating effects on senescence were then used in a new bioinformatic structure-function screen to identify common structural motifs. In total, 90 molecules displayed altered CDKN2A expression at one or other dose, of which 15 also displayed effects on SAB positivity in primary human dermal fibroblasts. Of these, 3 were associated with increased SAB activity, and 11 with reduced activity. The female synthetic sex hormones-diethylstilboestrol, ethynyl estradiol and levonorgestrel-were all associated with a reduction in aspects of the senescence phenotype in male cells, with no effects visible in female cells. Finally, we identified that the 30 compounds that decreased CDKN2A activity the most had a common substructure linked to this function. Our results suggest that several drugs licensed for other indications may warrant exploration as future senotherapies, but that different donors and potentially different sexes may respond differently to senotherapeutic compounds. This underlines the importance of considering donor-related characteristics when designing drug screening platforms.
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Affiliation(s)
- Laura R Bramwell
- RNA-Mediated Mechanisms of Disease Group, Department of Clinical and Biomedical Sciences (Medical School), Faculty of Health and Life Sciences, University of Exeter, Exeter EX2 5DW, UK
| | - Ryan Frankum
- RNA-Mediated Mechanisms of Disease Group, Department of Clinical and Biomedical Sciences (Medical School), Faculty of Health and Life Sciences, University of Exeter, Exeter EX2 5DW, UK
| | - Lorna W Harries
- RNA-Mediated Mechanisms of Disease Group, Department of Clinical and Biomedical Sciences (Medical School), Faculty of Health and Life Sciences, University of Exeter, Exeter EX2 5DW, UK
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3
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Kaneko H, Maezawa Y, Tsukagoshi-Yamaguchi A, Koshizaka M, Takada-Watanabe A, Nakamura R, Funayama S, Aono K, Teramoto N, Sawada D, Maeda Y, Minamizuka T, Hayashi A, Ide K, Ide S, Shoji M, Kitamoto T, Takemoto M, Kato H, Yokote K. Sex differences in symptom presentation and their impact on diagnostic accuracy in Werner syndrome. Geriatr Gerontol Int 2024; 24:161-167. [PMID: 38062994 DOI: 10.1111/ggi.14752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 10/27/2023] [Accepted: 11/09/2023] [Indexed: 01/05/2024]
Abstract
AIM Whether sex differences exist in hereditary progeroid syndromes remains unclear. In this study, we investigated sex differences in patients with Werner syndrome (WS), a model of human aging, using patient data at the time of diagnosis. METHODS The presence of six cardinal signs in the diagnostic criteria was retrospectively evaluated. RESULTS We found that the percentage of patients with all cardinal signs was higher in males than in females (54.2% vs. 21.2%). By the age of 40 years, 57.1% of male patients with WS presented with all the cardinal signs, whereas none of the female patients developed all of them. In particular, the frequency of having a high-pitched, hoarse voice, a characteristic of WS, was lower in female patients. The positive and negative predictive values for clinical diagnosis were 100% for males and females, indicating the helpfulness of diagnostic criteria regardless of sex. More female patients than male (86.7% vs. 64%) required genetic testing for their diagnosis because their clinical symptoms were insufficient, suggesting the importance of genetic testing for females even if they do not show typical symptoms of WS. Finally, the frequency of abnormal voice was lower in patients with WS harboring the c.3139-1G > C homozygous mutation. CONCLUSION These results indicate, for the first time, that there are sex differences in the phenotypes of hereditary progeroid syndromes. The analysis of this mechanism in this human model of aging may lead to the elucidation of sex differences in the various symptoms of normal human aging. Geriatr Gerontol Int 2024; 24: 161-167.
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Affiliation(s)
- Hiyori Kaneko
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Yoshiro Maezawa
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Ayano Tsukagoshi-Yamaguchi
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Masaya Koshizaka
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Aki Takada-Watanabe
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Rito Nakamura
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Shinichiro Funayama
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Kazuto Aono
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Naoya Teramoto
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Daisuke Sawada
- Department of Pediatrics, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Yukari Maeda
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Takuya Minamizuka
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Aiko Hayashi
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Kana Ide
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Shintaro Ide
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Mayumi Shoji
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Takumi Kitamoto
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Minoru Takemoto
- Department of Diabetes, Metabolism and Endocrinology, International University of Health and Welfare, Chiba, Japan
| | - Hisaya Kato
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Koutaro Yokote
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
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4
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Hahn MW, Peña-Garcia Y, Wang RJ. The 'faulty male' hypothesis for sex-biased mutation and disease. Curr Biol 2023; 33:R1166-R1172. [PMID: 37989088 DOI: 10.1016/j.cub.2023.09.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
Biological differences between males and females lead to many differences in physiology, disease, and overall health. One of the most prominent disparities is in the number of germline mutations passed to offspring: human males transmit three times as many mutations as do females. While the classic explanation for this pattern invokes differences in post-puberty germline replication between the sexes, recent whole-genome evidence in humans and other mammals has cast doubt on this mechanism. Here, we review recent work that is inconsistent with a replication-driven model of male-biased mutation, and propose an alternative, 'faulty male' hypothesis. This model proposes that males are less able to repair and/or protect DNA from damage compared to females. Importantly, we suggest that this new model for male-biased mutation may also help to explain several pronounced differences between the sexes in cancer, aging, and DNA repair. Although the detailed contributions of genetic, epigenetic, and hormonal influences of biological sex on mutation remain to be fully understood, a reconsideration of the mechanisms underlying these differences will lead to a deeper understanding of evolution and disease.
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Affiliation(s)
- Matthew W Hahn
- Department of Biology, Indiana University, 1001 E. 3(rd) Street, Bloomington, IN 47405, USA; Department of Computer Science, 700 N. Woodlawn Avenue, Bloomington, IN 47405, USA.
| | - Yadira Peña-Garcia
- Department of Biology, Indiana University, 1001 E. 3(rd) Street, Bloomington, IN 47405, USA
| | - Richard J Wang
- Department of Biology, Indiana University, 1001 E. 3(rd) Street, Bloomington, IN 47405, USA; Department of Computer Science, 700 N. Woodlawn Avenue, Bloomington, IN 47405, USA
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5
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Noh B, Blasco‐Conesa MP, Rahman SM, Monga S, Ritzel R, Guzman G, Lai Y, Ganesh BP, Urayama A, McCullough LD, Moruno‐Manchon JF. Iron overload induces cerebral endothelial senescence in aged mice and in primary culture in a sex-dependent manner. Aging Cell 2023; 22:e13977. [PMID: 37675802 PMCID: PMC10652299 DOI: 10.1111/acel.13977] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 08/13/2023] [Accepted: 08/16/2023] [Indexed: 09/08/2023] Open
Abstract
Iron imbalance in the brain negatively affects brain function. With aging, iron levels increase in the brain and contribute to brain damage and neurological disorders. Changes in the cerebral vasculature with aging may enhance iron entry into the brain parenchyma, leading to iron overload and its deleterious consequences. Endothelial senescence has emerged as an important contributor to age-related changes in the cerebral vasculature. Evidence indicates that iron overload may induce senescence in cultured cell lines. Importantly, cells derived from female human and mice generally show enhanced senescence-associated phenotype, compared with males. Thus, we hypothesize that cerebral endothelial cells (CEC) derived from aged female mice are more susceptible to iron-induced senescence, compared with CEC from aged males. We found that aged female mice, but not males, showed cognitive deficits when chronically treated with ferric citrate (FC), and their brains and the brain vasculature showed senescence-associated phenotype. We also found that primary culture of CEC derived from aged female mice, but not male-derived CEC, exhibited senescence-associated phenotype when treated with FC. We identified that the transmembrane receptor Robo4 was downregulated in the brain vasculature and in cultured primary CEC derived from aged female mice, compared with those from male mice. We discovered that Robo4 downregulation contributed to enhanced vulnerability to FC-induced senescence. Thus, our study identifies Robo4 downregulation as a driver of senescence induced by iron overload in primary culture of CEC and a potential risk factor of brain vasculature impairment and brain dysfunction.
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Affiliation(s)
- Brian Noh
- Department of NeurologyMcGovern Medical School at the University of Texas Health Science Center at HoustonHoustonTexasUSA
| | - Maria Pilar Blasco‐Conesa
- Department of NeurologyMcGovern Medical School at the University of Texas Health Science Center at HoustonHoustonTexasUSA
| | - Syed Mushfiqur Rahman
- Department of NeurologyMcGovern Medical School at the University of Texas Health Science Center at HoustonHoustonTexasUSA
| | - Sheelu Monga
- Department of NeurologyMcGovern Medical School at the University of Texas Health Science Center at HoustonHoustonTexasUSA
| | - Rodney Ritzel
- Department of NeurologyMcGovern Medical School at the University of Texas Health Science Center at HoustonHoustonTexasUSA
| | - Gary Guzman
- Department of NeurologyMcGovern Medical School at the University of Texas Health Science Center at HoustonHoustonTexasUSA
| | - Yun‐Ju Lai
- Department of NeurologyMcGovern Medical School at the University of Texas Health Science Center at HoustonHoustonTexasUSA
- Solomont School of NursingZuckerberg College of Health SciencesUniversity of Massachusetts LowellLowellMassachusettsUSA
| | - Bhanu Priya Ganesh
- Department of NeurologyMcGovern Medical School at the University of Texas Health Science Center at HoustonHoustonTexasUSA
| | - Akihiko Urayama
- Department of NeurologyMcGovern Medical School at the University of Texas Health Science Center at HoustonHoustonTexasUSA
| | - Louise D. McCullough
- Department of NeurologyMcGovern Medical School at the University of Texas Health Science Center at HoustonHoustonTexasUSA
| | - Jose Felix Moruno‐Manchon
- Department of NeurologyMcGovern Medical School at the University of Texas Health Science Center at HoustonHoustonTexasUSA
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6
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Handwerk L, Schreier HK, Kraft D, Shreder K, Hemmersbach R, Hauslage J, Bonig H, Wiesmüller L, Fournier C, Rall-Scharpf M. Simulating Space Conditions Evokes Different DNA Damage Responses in Immature and Mature Cells of the Human Hematopoietic System. Int J Mol Sci 2023; 24:13761. [PMID: 37762064 PMCID: PMC10531023 DOI: 10.3390/ijms241813761] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
The impact of space radiation and microgravity on DNA damage responses has been discussed controversially, largely due to the variety of model systems engaged. Here, we performed side-by-side analyses of human hematopoietic stem/progenitor cells (HSPC) and peripheral blood lymphocytes (PBL) cultivated in a 2D clinostat to simulate microgravity before, during and after photon and particle irradiation. We demonstrate that simulated microgravity (SMG) accelerates the early phase of non-homologous end joining (NHEJ)-mediated repair of simple, X-ray-induced DNA double-strand breaks (DSBs) in PBL, while repair kinetics in HSPC remained unaltered. Repair acceleration was lost with increasing LET of ion exposures, which increases the complexity of DSBs, precluding NHEJ and requiring end resection for successful repair. Such cell-type specific effect of SMG on DSB repair was dependent on the NF-кB pathway pre-activated in PBL but not HSPC. Already under unperturbed growth conditions HSPC and PBL suffered from SMG-induced replication stress associated with accumulation of single-stranded DNA and DSBs, respectively. We conclude that in PBL, SMG-induced DSBs promote repair of radiation-induced damage in an adaptive-like response. HSPC feature SMG-induced single-stranded DNA and FANCD2 foci, i.e., markers of persistent replication stress and senescence that may contribute to a premature decline of the immune system in space.
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Affiliation(s)
- Leonie Handwerk
- Department of Biophysics, GSI Helmholtz Center for Heavy Ion Research, 64291 Darmstadt, Germany
| | | | - Daniela Kraft
- Department of Biophysics, GSI Helmholtz Center for Heavy Ion Research, 64291 Darmstadt, Germany
| | - Kateryna Shreder
- Department of Biophysics, GSI Helmholtz Center for Heavy Ion Research, 64291 Darmstadt, Germany
| | - Ruth Hemmersbach
- Department of Gravitational Biology, German Aerospace Center, Institute of Aerospace Medicine, 51147 Cologne, Germany; (R.H.)
| | - Jens Hauslage
- Department of Gravitational Biology, German Aerospace Center, Institute of Aerospace Medicine, 51147 Cologne, Germany; (R.H.)
| | - Halvard Bonig
- Institute for Transfusion Medicine and Immunohematology, Johann Wolfgang Goethe-University Hospital, and German Red Cross Blood Service, Baden-Wuerttemberg–Hessen, 60528 Frankfurt, Germany
| | - Lisa Wiesmüller
- Department of Obstetrics and Gynecology, Ulm University, 89075 Ulm, Germany
| | - Claudia Fournier
- Department of Biophysics, GSI Helmholtz Center for Heavy Ion Research, 64291 Darmstadt, Germany
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7
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Leung E, Taskina D, Schwab N, Hazrati LN. BRCA1 heterozygosity promotes DNA damage-induced senescence in a sex-specific manner following repeated mild traumatic brain injury. Front Neurosci 2023; 17:1225226. [PMID: 37638313 PMCID: PMC10450634 DOI: 10.3389/fnins.2023.1225226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 07/21/2023] [Indexed: 08/29/2023] Open
Abstract
Emerging evidence suggests cellular senescence, as a consequence of excess DNA damage and deficient repair, to be a driver of brain dysfunction following repeated mild traumatic brain injury (rmTBI). This study aimed to further investigate the role of deficient DNA repair, specifically BRCA1-related repair, on DNA damage-induced senescence. BRCA1, a repair protein involved in maintaining genomic integrity with multiple roles in the central nervous system, was previously reported to be significantly downregulated in post-mortem brains with a history of rmTBI. Here we examined the effects of impaired BRCA1-related repair on DNA damage-induced senescence and outcomes 1-week post-rmTBI using mice with a heterozygous knockout for BRCA1 in a sex-segregated manner. Altered BRCA1 repair with rmTBI resulted in altered anxiety-related behaviours in males and females using elevated zero maze and contextual fear conditioning. Evaluating molecular markers associated with DNA damage signalling and senescence-related pathways revealed sex-specific differences attributed to BRCA1, where females exhibited elevated DNA damage, impaired DNA damage signalling, and dampened senescence onset compared to males. Overall, the results from this study highlight sex-specific consequences of aberrant DNA repair on outcomes post-injury, and further support a need to develop sex-specific treatments following rmTBI.
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Affiliation(s)
- Emily Leung
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, ON, Canada
| | - Daria Taskina
- Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, ON, Canada
| | - Nicole Schwab
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, ON, Canada
| | - Lili-Naz Hazrati
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, ON, Canada
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8
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Abstract
Senescence is a complex cell state characterized by stable cell cycle arrest and a unique secretory pattern known as the senescence-associated secretory phenotype (SASP). The SASP factors, which are heterogeneous and tissue specific, normally include chemokines, cytokines, growth factors, adhesion molecules, and lipid components that can lead to multiple age-associated disorders by eliciting local and systemic consequences. The skeleton is a highly dynamic organ that changes constantly in shape and composition. Senescent cells in bone and bone marrow produce diverse SASP factors that induce alterations of the skeleton through paracrine effects. Herein, we refer to bone cell-associated SASP as "bone-SASP." In this review, we describe current knowledge of cellular senescence and SASP, focusing on the role of senescent cells in mediating bone pathologies during natural aging and premature aging syndromes. We also summarize the role of cellular senescence and the bone-SASP in glucocorticoids-induced bone damage. In addition, we discuss the role of bone-SASP in the development of osteoarthritis, highlighting the mechanisms by which bone-SASP drives subchondral bone changes in metabolic syndrome-associated osteoarthritis.
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Affiliation(s)
- Ching-Lien Fang
- Department of Orthopaedic Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Bin Liu
- Department of Orthopaedic Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Mei Wan
- Department of Orthopaedic Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Department of Orthopaedic Surgery, The Johns Hopkins University School of Medicine, Ross Building, Room 209, 720 Rutland Avenue, Baltimore, MD, 21205, USA.
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9
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Yang W, Rubin JB. Accounting for sex differences as a continuous variable in cancer treatments. RESEARCH SQUARE 2023:rs.3.rs-3120372. [PMID: 37461646 PMCID: PMC10350164 DOI: 10.21203/rs.3.rs-3120372/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The significant sex differences that exist in cancer mechanisms, incidence, and survival, have yet to impact clinical practice. We propose that one barrier to translation is that sex differences in cancer phenotypes resemble sex differences in height: highly overlapping, but distinct, male and female population distributions that vary continuously between female- and male- skewed extremes. A consequence of this variance is that sex-specific treatments are rendered unrealistic, and our translational goal should be adaptation of treatment to the variable sex-effect on targetable pathways. To develop a tool that could advance this goal, we applied a Bayesian Nearest Neighbor (BNN) analysis to 8370 cancer transcriptomes from 26 different adult and 4 different pediatric cancer types to establish patient-specific Transcriptomic Indices (TI). TI precisely positions a patient's whole transcriptome on axes of mechanistic phenotypes like cell cycle signaling and immunity that exhibit skewing in the cancer population relative to sex-identified extremes (poles). Importantly, the TI approach reveals that even when TI values are identical, underlying mechanisms in male and female individuals can differ in identifiable ways. Thus, cancer type, patient sex, and TI value provides a novel and patient- specific mechanistic identifier that can be used for precision cancer treatment planning.
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Affiliation(s)
- Wei Yang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110
| | - Joshua B Rubin
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110
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10
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Wang P, Ouyang J, Jia Z, Zhang A, Yang Y. Roles of DNA damage in renal tubular epithelial cells injury. Front Physiol 2023; 14:1162546. [PMID: 37089416 PMCID: PMC10117683 DOI: 10.3389/fphys.2023.1162546] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 03/29/2023] [Indexed: 04/09/2023] Open
Abstract
The prevalence of renal diseases including acute kidney injury (AKI) and chronic kidney disease (CKD) is increasing worldwide. However, the pathogenesis of most renal diseases is still unclear and effective treatments are still lacking. DNA damage and the related DNA damage response (DDR) have been confirmed as common pathogenesis of acute kidney injury and chronic kidney disease. Reactive oxygen species (ROS) induced DNA damage is one of the most common types of DNA damage involved in the pathogenesis of acute kidney injury and chronic kidney disease. In recent years, several developments have been made in the field of DNA damage. Herein, we review the roles and developments of DNA damage and DNA damage response in renal tubular epithelial cell injury in acute kidney injury and chronic kidney disease. In this review, we conclude that focusing on DNA damage and DNA damage response may provide valuable diagnostic biomarkers and treatment strategies for renal diseases including acute kidney injury and chronic kidney disease.
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Affiliation(s)
- Peipei Wang
- Department of Nephrology, Children’s Hospital of Nanjing Medical University, Nanjing, China
- Nanjing Key Laboratory of Pediatrics, Children’s Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Key Laboratory of Pediatrics, Nanjing Medical University, Nanjing, China
| | - Jing Ouyang
- Department of Nephrology, Children’s Hospital of Nanjing Medical University, Nanjing, China
- Nanjing Key Laboratory of Pediatrics, Children’s Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Key Laboratory of Pediatrics, Nanjing Medical University, Nanjing, China
| | - Zhanjun Jia
- Department of Nephrology, Children’s Hospital of Nanjing Medical University, Nanjing, China
- Nanjing Key Laboratory of Pediatrics, Children’s Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Key Laboratory of Pediatrics, Nanjing Medical University, Nanjing, China
| | - Aihua Zhang
- Department of Nephrology, Children’s Hospital of Nanjing Medical University, Nanjing, China
- Nanjing Key Laboratory of Pediatrics, Children’s Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Key Laboratory of Pediatrics, Nanjing Medical University, Nanjing, China
- *Correspondence: Yunwen Yang, ; Aihua Zhang,
| | - Yunwen Yang
- Department of Nephrology, Children’s Hospital of Nanjing Medical University, Nanjing, China
- Nanjing Key Laboratory of Pediatrics, Children’s Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Key Laboratory of Pediatrics, Nanjing Medical University, Nanjing, China
- *Correspondence: Yunwen Yang, ; Aihua Zhang,
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11
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Tubić Vukajlović J, Simić I, Smiljanić Z, Grujičić D, Milošević-Djordjević O. Genome instability in peripheral blood lymphocytes of patients with heart failure and reduced ejection fraction. Mutagenesis 2023; 38:84-92. [PMID: 36738247 DOI: 10.1093/mutage/gead002] [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: 11/07/2022] [Accepted: 01/11/2023] [Indexed: 02/05/2023] Open
Abstract
Heart failure (HF) is a complex clinical condition characterized by functional and structural defects of the myocardium, but genetic and environmental factors are considered to play an important role in the development of the disease. In the present study, we investigated the genome instability (DNA and chromosomal damage) in patients with heart failure with reduced ejection fraction (HFrEF) ≤40% and its association with risk factors. The studied population included 48 individuals, of which 29 HFrEF patients (mean age 57.41 ± 5.74 years) and 19 healthy controls (mean age 57.63 ± 6.09 years). The genetic damage index in peripheral blood lymphocytes was analyzed using the comet assay, while micronuclei frequency and nuclear division index were analyzed using the cytokinesis-block micronucleus assay. Our results showed that HFrEF patients had a significantly higher genetic damage index compared with the healthy controls (P < .001). Cytokinesis-block micronucleus assay showed that the average micronucleus frequency in peripheral blood lymphocytes of patients was significantly higher, while the nuclear division index values were significantly lower than in controls (P < .01). Using multiple linear regression analysis, pathological state, ejection fraction, creatinine, glucose, associated disease, residence, proBNP, troponin, urea, ACE-inhibitors, and length of the drug therapy were identified as predictors of DNA and/or chromosomal damage in HF patients. We can conclude that DNA and chromosomal damage was increased in patients with HF, which may be a consequence of disease and/or drug therapy.
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Affiliation(s)
- Jovana Tubić Vukajlović
- University of Kragujevac, Faculty of Science, Department of Biology and Ecology, 34000 Kragujevac, Serbia
| | - Ivan Simić
- University of Kragujevac, Faculty of Medical Sciences, Department of Internal Medicine, 34000 Kragujevac, Serbia.,University Clinical Center Kragujevac, Department of Cardiology, 34000 Kragujevac, Serbia
| | - Zorica Smiljanić
- University Clinical Center Kragujevac, Department of Cardiology, 34000 Kragujevac, Serbia
| | - Darko Grujičić
- University of Kragujevac, Faculty of Science, Department of Biology and Ecology, 34000 Kragujevac, Serbia
| | - Olivera Milošević-Djordjević
- University of Kragujevac, Faculty of Science, Department of Biology and Ecology, 34000 Kragujevac, Serbia.,University of Kragujevac, Faculty of Medical Sciences, Department of Genetics, 34000 Kragujevac, Serbia
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The landscape of aging. SCIENCE CHINA LIFE SCIENCES 2022; 65:2354-2454. [PMID: 36066811 PMCID: PMC9446657 DOI: 10.1007/s11427-022-2161-3] [Citation(s) in RCA: 91] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 07/05/2022] [Indexed: 02/07/2023]
Abstract
Aging is characterized by a progressive deterioration of physiological integrity, leading to impaired functional ability and ultimately increased susceptibility to death. It is a major risk factor for chronic human diseases, including cardiovascular disease, diabetes, neurological degeneration, and cancer. Therefore, the growing emphasis on “healthy aging” raises a series of important questions in life and social sciences. In recent years, there has been unprecedented progress in aging research, particularly the discovery that the rate of aging is at least partly controlled by evolutionarily conserved genetic pathways and biological processes. In an attempt to bring full-fledged understanding to both the aging process and age-associated diseases, we review the descriptive, conceptual, and interventive aspects of the landscape of aging composed of a number of layers at the cellular, tissue, organ, organ system, and organismal levels.
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Evidence of Sex Differences in Cellular Senescence. Neurobiol Aging 2022; 120:88-104. [DOI: 10.1016/j.neurobiolaging.2022.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/30/2022] [Accepted: 08/30/2022] [Indexed: 11/20/2022]
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Xu P, Xu X, Liu J, Hu H, Shen H, Chen C. Association of single nucleotide polymorphisms in the nuclear respiratory factor-2 beta subunit-encoding GABPB1 gene with the occupational environment. Toxicol Ind Health 2022; 38:193-200. [PMID: 35343317 DOI: 10.1177/07482337221081923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
GABPB1, known as nuclear respiratory factor 2 (Nrf2), activates the mitochondrial genes that are responsible for antioxidant action and detoxification. Two single nucleotide polymorphisms (SNPs) of GABPB1, such as rs7181866 and rs8031031, were reported to be associated with the prevention of the increasing cancer risk caused by environmental deterioration. Between March 1 and May 1, 2018, human peripheral blood mononuclear cells (PBMCs) from a cohort of 300 volunteers working in adverse occupational environments were genotyped for the two SNPs in the present study. The SNP rs7181866 was found to be significantly greater in the male group than in the female group. Frequencies of SNP rs7181866 and bi-allele SNPs (rs7181866 + rs8031031) were significantly different between the <35-year-old group and the ≥35-year-old group. Further, multinomial logistic regression analysis of the occupational environments revealed the highest predictive frequency of SNPs for four environmental factors, of which chemical factors accounted for 15.33% rs7181866, physical factors accounted for 34.79% rs7181866 + rs8031031, physical + chemical factors accounted for 39.5% rs8031031, and unknown factors accounted for 26.5% rs7181866 + rs8031031. In conclusion, the G allele of rs7181866 was found to be significantly more susceptible than the rs8031031 allele under adverse occupational environmental factors, and physical factors such as noise, which appear to play vital roles in causing SNP mutations.
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Affiliation(s)
- Pei Xu
- China Jiliang University, Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine; College of Innovation, Hangzhou, China
| | - Xingjie Xu
- China Jiliang University, Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine; College of Innovation, Hangzhou, China
| | - Jun Liu
- China Jiliang University, Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine; College of Innovation, Hangzhou, China
| | - Huajun Hu
- China Jiliang University, Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine; College of Innovation, Hangzhou, China
| | | | - Chun Chen
- China Jiliang University, Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine; College of Innovation, Hangzhou, China
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