1
|
Leone R, Zuglian C, Brambilla R, Morella I. Understanding copy number variations through their genes: a molecular view on 16p11.2 deletion and duplication syndromes. Front Pharmacol 2024; 15:1407865. [PMID: 38948459 PMCID: PMC11211608 DOI: 10.3389/fphar.2024.1407865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 05/16/2024] [Indexed: 07/02/2024] Open
Abstract
Neurodevelopmental disorders (NDDs) include a broad spectrum of pathological conditions that affect >4% of children worldwide, share common features and present a variegated genetic origin. They include clinically defined diseases, such as autism spectrum disorders (ASD), attention-deficit/hyperactivity disorder (ADHD), motor disorders such as Tics and Tourette's syndromes, but also much more heterogeneous conditions like intellectual disability (ID) and epilepsy. Schizophrenia (SCZ) has also recently been proposed to belong to NDDs. Relatively common causes of NDDs are copy number variations (CNVs), characterised by the gain or the loss of a portion of a chromosome. In this review, we focus on deletions and duplications at the 16p11.2 chromosomal region, associated with NDDs, ID, ASD but also epilepsy and SCZ. Some of the core phenotypes presented by human carriers could be recapitulated in animal and cellular models, which also highlighted prominent neurophysiological and signalling alterations underpinning 16p11.2 CNVs-associated phenotypes. In this review, we also provide an overview of the genes within the 16p11.2 locus, including those with partially known or unknown function as well as non-coding RNAs. A particularly interesting interplay was observed between MVP and MAPK3 in modulating some of the pathological phenotypes associated with the 16p11.2 deletion. Elucidating their role in intracellular signalling and their functional links will be a key step to devise novel therapeutic strategies for 16p11.2 CNVs-related syndromes.
Collapse
Affiliation(s)
- Roberta Leone
- Università di Pavia, Dipartimento di Biologia e Biotecnologie “Lazzaro Spallanzani”, Pavia, Italy
| | - Cecilia Zuglian
- Università di Pavia, Dipartimento di Biologia e Biotecnologie “Lazzaro Spallanzani”, Pavia, Italy
| | - Riccardo Brambilla
- Università di Pavia, Dipartimento di Biologia e Biotecnologie “Lazzaro Spallanzani”, Pavia, Italy
- Cardiff University, School of Biosciences, Neuroscience and Mental Health Innovation Institute, Cardiff, United Kingdom
| | - Ilaria Morella
- Cardiff University, School of Biosciences, Neuroscience and Mental Health Innovation Institute, Cardiff, United Kingdom
| |
Collapse
|
2
|
Aggarwal S, Wang Z, Rincon Fernandez Pacheco D, Rinaldi A, Rajewski A, Callemeyn J, Van Loon E, Lamarthée B, Covarrubias AE, Hou J, Yamashita M, Akiyama H, Karumanchi SA, Svendsen CN, Noble PW, Jordan SC, Breunig JJ, Naesens M, Cippà PE, Kumar S. SOX9 switch links regeneration to fibrosis at the single-cell level in mammalian kidneys. Science 2024; 383:eadd6371. [PMID: 38386758 DOI: 10.1126/science.add6371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 01/11/2024] [Indexed: 02/24/2024]
Abstract
The steps governing healing with or without fibrosis within the same microenvironment are unclear. After acute kidney injury (AKI), injured proximal tubular epithelial cells activate SOX9 for self-restoration. Using a multimodal approach for a head-to-head comparison of injury-induced SOX9 lineages, we identified a dynamic SOX9 switch in repairing epithelia. Lineages that regenerated epithelia silenced SOX9 and healed without fibrosis (SOX9on-off). By contrast, lineages with unrestored apicobasal polarity maintained SOX9 activity in sustained efforts to regenerate, which were identified as a SOX9on-on Cadherin6pos cell state. These reprogrammed cells generated substantial single-cell WNT activity to provoke a fibroproliferative response in adjacent fibroblasts, driving AKI to chronic kidney disease. Transplanted human kidneys displayed similar SOX9/CDH6/WNT2B responses. Thus, we have uncovered a sensor of epithelial repair status, the activity of which determines regeneration with or without fibrosis.
Collapse
Affiliation(s)
- Shikhar Aggarwal
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Zhanxiang Wang
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - David Rincon Fernandez Pacheco
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Anna Rinaldi
- Division of Nephrology, Ente Ospedaliero Cantonale, CH-6900 Lugano, Switzerland
| | - Alex Rajewski
- Applied Genomics, Computation, and Translational Core, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jasper Callemeyn
- Department of Microbiology, Immunology and Transplantation, KU Leuven, BE-3000 Leuven, Belgium
| | - Elisabet Van Loon
- Department of Microbiology, Immunology and Transplantation, KU Leuven, BE-3000 Leuven, Belgium
| | - Baptiste Lamarthée
- Department of Microbiology, Immunology and Transplantation, KU Leuven, BE-3000 Leuven, Belgium
| | - Ambart Ester Covarrubias
- Division of Nephrology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jean Hou
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Michifumi Yamashita
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Haruhiko Akiyama
- Department of Orthopaedic Surgery, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan
| | - S Ananth Karumanchi
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Division of Nephrology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Clive N Svendsen
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Paul W Noble
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Women's Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Stanley C Jordan
- Division of Nephrology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Joshua J Breunig
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Maarten Naesens
- Department of Microbiology, Immunology and Transplantation, KU Leuven, BE-3000 Leuven, Belgium
| | - Pietro E Cippà
- Division of Nephrology, Ente Ospedaliero Cantonale, CH-6900 Lugano, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, CH-6900 Lugano, Switzerland
| | - Sanjeev Kumar
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Division of Nephrology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| |
Collapse
|
3
|
Haller M, Yin Y, Haller G, Li T, Li Q, Lamb LE, Ma L. Streamlined identification of clinically and functionally relevant genetic regulators of lower-tract urogenital development. Proc Natl Acad Sci U S A 2024; 121:e2309466121. [PMID: 38300866 PMCID: PMC10861909 DOI: 10.1073/pnas.2309466121] [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: 06/06/2023] [Accepted: 12/18/2023] [Indexed: 02/03/2024] Open
Abstract
Congenital anomalies of the lower genitourinary (LGU) tract are frequently comorbid due to genetically linked developmental pathways, and are among the most common yet most socially stigmatized congenital phenotypes. Genes involved in sexual differentiation are prime candidates for developmental anomalies of multiple LGU organs, but insufficient prospective screening tools have prevented the rapid identification of causative genes. Androgen signaling is among the most influential modulators of LGU development. The present study uses SpDamID technology in vivo to generate a comprehensive map of the pathways actively regulated by the androgen receptor (AR) in the genitalia in the presence of the p300 coactivator, identifying wingless/integrated (WNT) signaling as a highly enriched AR-regulated pathway in the genitalia. Transcription factor (TF) hits were then assayed for sexually dimorphic expression at two critical time points and also cross-referenced to a database of clinically relevant copy number variations to identify 252 TFs exhibiting copy variation in patients with LGU phenotypes. A subset of 54 TFs was identified for which LGU phenotypes are statistically overrepresented as a proportion of total observed phenotypes. The 252 TF hitlist was then subjected to a functional screen to identify hits whose silencing affects genital mesenchymal growth rates. Overlap of these datasets results in a refined list of 133 TFs of both functional and clinical relevance to LGU development, 31 of which are top priority candidates, including the well-documented renal progenitor regulator, Sall1. Loss of Sall1 was examined in vivo and confirmed to be a powerful regulator of LGU development.
Collapse
Affiliation(s)
- Meade Haller
- Division of Dermatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO63110
| | - Yan Yin
- Division of Dermatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO63110
| | - Gabe Haller
- Department of Neurosurgery, Washington University School of Medicine, St. Louis, MO63110
| | - Tian Li
- Division of Dermatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO63110
| | - Qiufang Li
- Division of Dermatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO63110
| | - Laura E. Lamb
- Department of Urology, William Beaumont School of Medicine, Oakland University, Rochester, MI48309
| | - Liang Ma
- Division of Dermatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO63110
| |
Collapse
|
4
|
Chung WK, Herrera FF. Health supervision for children and adolescents with 16p11.2 deletion syndrome. Cold Spring Harb Mol Case Stud 2023; 9:a006316. [PMID: 38050025 PMCID: PMC10815286 DOI: 10.1101/mcs.a006316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/28/2023] [Indexed: 12/06/2023] Open
Abstract
Rare genetic conditions are challenging for the primary care provider to manage without proper guidelines. This clinical review is designed to assist the pediatrician, family physician, or internist in the primary care setting to manage the complexities of 16p11.2 deletion syndrome. A multidisciplinary medical home with the primary care provider leading the care and armed with up-to-date guidelines will prove most helpful to the rare genetic patient population. A special focus on technology to fill gaps in deficits, review of case studies on novel medical treatments, and involvement with the educational system for advocacy with an emphasis on celebrating diversity will serve the rare genetic syndrome population well.
Collapse
Affiliation(s)
- Wendy K Chung
- Harvard Medical School and Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | | |
Collapse
|
5
|
Eisenberg ML, Esteves SC, Lamb DJ, Hotaling JM, Giwercman A, Hwang K, Cheng YS. Male infertility. Nat Rev Dis Primers 2023; 9:49. [PMID: 37709866 DOI: 10.1038/s41572-023-00459-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/09/2023] [Indexed: 09/16/2023]
Abstract
Clinical infertility is the inability of a couple to conceive after 12 months of trying. Male factors are estimated to contribute to 30-50% of cases of infertility. Infertility or reduced fertility can result from testicular dysfunction, endocrinopathies, lifestyle factors (such as tobacco and obesity), congenital anatomical factors, gonadotoxic exposures and ageing, among others. The evaluation of male infertility includes detailed history taking, focused physical examination and selective laboratory testing, including semen analysis. Treatments include lifestyle optimization, empirical or targeted medical therapy as well as surgical therapies that lead to measurable improvement in fertility. Although male infertility is recognized as a disease with effects on quality of life for both members of the infertile couple, fewer data exist on specific quantification and impact compared with other health-related conditions.
Collapse
Affiliation(s)
- Michael L Eisenberg
- Department of Urology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Obstetrics & Gynecology, Stanford University School of Medicine, Stanford, CA, USA.
| | - Sandro C Esteves
- ANDROFERT Andrology and Human Reproduction Clinic, Campinas, Brazil
- Division of Urology, Department of Surgery, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
| | - Dolores J Lamb
- Center for Reproductive Genomics, Weill Cornell Medical College, New York, NY, USA
- Englander Institute for Precision Medicine, Weill Cornell Medical College, New York, NY, USA
- Department of Urology, Weill Cornell Medical College, New York, NY, USA
| | - James M Hotaling
- Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | | | - Kathleen Hwang
- University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Yu-Sheng Cheng
- Department of Urology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| |
Collapse
|
6
|
Nordenskjöld A, Arkani S, Pettersson M, Winberg J, Cao J, Fossum M, Anderberg M, Barker G, Holmdahl G, Lundin J. Copy number variants suggest different molecular pathways for the pathogenesis of bladder exstrophy. Am J Med Genet A 2023; 191:378-390. [PMID: 36349425 PMCID: PMC10100507 DOI: 10.1002/ajmg.a.63031] [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: 07/04/2022] [Revised: 08/05/2022] [Accepted: 10/07/2022] [Indexed: 11/10/2022]
Abstract
Bladder exstrophy is a rare congenital malformation leaving the urinary bladder open in the midline of the abdomen at birth. There is a clear genetic background with chromosome aberrations, but so far, no consistent findings apart from 22q11-duplications detected in about 2%-3% of all patients. Some genes are implicated like the LZTR1, ISL1, CELSR3, and the WNT3 genes, but most are not explained molecularly. We have performed chromosomal microarray analysis on a cohort of 140 persons born with bladder exstrophy to look for submicroscopic chromosomal deletions and duplications. Pathogenic or possibly pathogenic microdeletions or duplications were found in 16 patients (11.4%) and further 9 with unknown significance. Two findings were in regions linked to known syndromes, two findings involved the same gene (MCC), and all other findings were unique. A closer analysis suggests a few gene networks that are involved in the pathogenesis of bladder exstrophy; the WNT-signaling pathway, the chromosome 22q11 region, the RIT2 and POU families, and involvement of the Golgi apparatus. Bladder exstrophy is a rare malformation and is reported to be associated with several chromosome aberrations. Our data suggest involvement of some specific molecular pathways.
Collapse
Affiliation(s)
- Agneta Nordenskjöld
- Department of Women's and Children's Health, and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Pediatric Surgery, Astrid Lindgren Children Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Samara Arkani
- Department of Women's and Children's Health, and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Urology, Danderyds Hospital, Danderyd, Sweden
| | - Maria Pettersson
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Johanna Winberg
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Jia Cao
- Department of Women's and Children's Health, and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Magdalena Fossum
- Department of Women's and Children's Health, and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Pediatric Surgery, Copenhagen University, Righospitalet, København, Denmark
| | - Magnus Anderberg
- Department of Pediatric Surgery, Skåne University Hospital, Lund, Sweden.,Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Gillian Barker
- Department of Pediatric Surgery, Uppsala Academic Hospital, Uppsala, Sweden
| | - Gundela Holmdahl
- Department of Women's and Children's Health, and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Pediatric Surgery, Astrid Lindgren Children Hospital, Karolinska University Hospital, Stockholm, Sweden.,Sahlgrenska Academy, Women's and Children's Health, Gothenburg, Sweden.,Department of Pediatric Surgery, Queen Silvia's Children's Hospital, Gothenburg, Sweden
| | - Johanna Lundin
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
7
|
Ruthig VA, Lamb DJ. Modeling development of genitourinary birth defects to understand disruption due to changes in gene dosage. AMERICAN JOURNAL OF CLINICAL AND EXPERIMENTAL UROLOGY 2022; 10:412-424. [PMID: 36636694 PMCID: PMC9831917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 12/25/2022] [Indexed: 01/14/2023]
Abstract
Genitourinary development is a delicately orchestrated process that begins in the embryo. Once complete, the genitourinary system is a collection of functionally disparate organs spread throughout the abdominal and pelvic regions. These distinct organs are interconnected through an elaborate duct system which aggregates the organs' products to a common exit point. The complicated nature of the genitourinary system makes it highly susceptible to developmental disruptions that produce anomalies. In fact, genitourinary anomalies are among the most common class of human birth defects. Aside from congenital anomalies of the kidney and urinary tract (CAKUT), for males, these birth defects can also occur in the penis (hypospadias) and testis (cryptorchism), which impact male fertility and male mental health. As genetic technology has advanced, it has become clear that a subset of cases of genitourinary birth defects are due to gene variation causing dosage changes in critical regulatory genes. Here we first review the parallels between human and mouse genitourinary development. We then demonstrate how translational research leverages mouse models of human gene variation cases to advance mechanistic understanding of causation in genitourinary birth defects. We close with a view to the future highlighting upcoming technologies that will provide a deeper understanding of gene variation affecting regulation of genitourinary development, which should ultimately advance treatment options for patients.
Collapse
Affiliation(s)
- Victor A Ruthig
- Department of Urology, Weill Cornell MedicineNew York, NY, USA,Sexual Medicine Laboratory, Weill Cornell MedicineNew York, NY, USA
| | - Dolores J Lamb
- Department of Urology, Weill Cornell MedicineNew York, NY, USA,Center for Reproductive Genomics, Weill Cornell MedicineNew York, NY, USA,Englander Institute for Precision Medicine, Weill Cornell MedicineNew York, NY, USA
| |
Collapse
|
8
|
Seth A, Rivera A, Choi IS, Medina-Martinez O, Lewis S, O’Neill M, Ridgeway A, Moore J, Jorgez C, Lamb DJ. Gene dosage changes in KCTD13 result in penile and testicular anomalies via diminished androgen receptor function. FASEB J 2022; 36:e22567. [PMID: 36196997 PMCID: PMC10538574 DOI: 10.1096/fj.202200558r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/27/2022] [Accepted: 09/13/2022] [Indexed: 01/13/2023]
Abstract
Despite the high prevalence of hypospadias and cryptorchidism, the genetic basis for these conditions is only beginning to be understood. Using array-comparative-genomic-hybridization (aCGH), potassium-channel-tetramerization-domain-containing-13 (KCTD13) encoded at 16p11.2 was identified as a candidate gene involved in hypospadias, cryptorchidism and other genitourinary (GU) tract anomalies. Copy number variants (CNVs) at 16p11.2 are among the most common syndromic genomic variants identified to date. Many patients with CNVs at this locus exhibit GU and/or neurodevelopmental phenotypes. KCTD13 encodes a substrate-specific adapter of a BCR (BTB-CUL3-RBX1) E3-ubiquitin-protein-ligase complex (BCR (BTB-CUL3-RBX1) E3-ubiquitin-protein-ligase complex (B-cell receptor (BCR) [BTB (the BTB domain is a conserved motif involved in protein-protein interactions) Cullin3 complex RING protein Rbx1] E3-ubiqutin-protein-ligase complex), which has essential roles in the regulation of cellular cytoskeleton, migration, proliferation, and neurodevelopment; yet its role in GU development is unknown. The prevalence of KCTD13 CNVs in patients with GU anomalies (2.58%) is significantly elevated when compared with patients without GU anomalies or in the general population (0.10%). KCTD13 is robustly expressed in the developing GU tract. Loss of KCTD13 in cell lines results in significantly decreased levels of nuclear androgen receptor (AR), suggesting that loss of KCTD13 affects AR sub-cellular localization. Kctd13 haploinsufficiency and homozygous deletion in mice cause a significant increase in the incidence of cryptorchidism and micropenis. KCTD13-deficient mice exhibit testicular and penile abnormalities together with significantly reduced levels of nuclear AR and SOX9. In conclusion, gene-dosage changes of murine Kctd13 diminish nuclear AR sub-cellular localization, as well as decrease SOX9 expression levels which likely contribute in part to the abnormal GU tract development in Kctd13 mouse models and in patients with CNVs in KCTD13.
Collapse
Affiliation(s)
- Abhishek Seth
- Scott Department of Urology, Baylor College of Medicine, Houston, TX, 77030
- Center for Reproductive Medicine, Baylor College of Medicine, Houston, TX, 77030
- Department of Surgery, Nemours Children’s Hospital, Orlando, Florida 32827
| | - Armando Rivera
- Scott Department of Urology, Baylor College of Medicine, Houston, TX, 77030
- Center for Reproductive Medicine, Baylor College of Medicine, Houston, TX, 77030
| | - In-Seon Choi
- Scott Department of Urology, Baylor College of Medicine, Houston, TX, 77030
- Center for Reproductive Medicine, Baylor College of Medicine, Houston, TX, 77030
| | - Olga Medina-Martinez
- Scott Department of Urology, Baylor College of Medicine, Houston, TX, 77030
- Center for Reproductive Medicine, Baylor College of Medicine, Houston, TX, 77030
| | - Shaye Lewis
- Scott Department of Urology, Baylor College of Medicine, Houston, TX, 77030
- Center for Reproductive Medicine, Baylor College of Medicine, Houston, TX, 77030
| | - Marisol O’Neill
- Center for Reproductive Medicine, Baylor College of Medicine, Houston, TX, 77030
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030
| | - Alex Ridgeway
- Center for Reproductive Medicine, Baylor College of Medicine, Houston, TX, 77030
| | - Joshua Moore
- Center for Reproductive Medicine, Baylor College of Medicine, Houston, TX, 77030
| | - Carolina Jorgez
- Scott Department of Urology, Baylor College of Medicine, Houston, TX, 77030
- Center for Reproductive Medicine, Baylor College of Medicine, Houston, TX, 77030
| | - Dolores J. Lamb
- Scott Department of Urology, Baylor College of Medicine, Houston, TX, 77030
- Center for Reproductive Medicine, Baylor College of Medicine, Houston, TX, 77030
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030
- The James Buchanan Brady Foundation Department of Urology, Center for Reproductive Genomics and Englander Institute for Personalized Medicine, Weill Cornell Medical College
| |
Collapse
|
9
|
Construction of Copy Number Variation Map Identifies Small Regions of Overlap and Candidate Genes for Atypical Female Genitalia Development. REPRODUCTIVE MEDICINE 2022. [DOI: 10.3390/reprodmed3020014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Copy number variations (CNVs) have been implicated in various conditions of differences of sexual development (DSD). Generally, larger genomic aberrations are more often considered disease-causing or clinically relevant, but over time, smaller CNVs have been associated with various forms of DSD. The main objective of this study is to identify small CNVs and the smallest regions of overlap (SROs) in patients with atypical female genitalia (AFG) and build a CNV map of AFG. We queried the DECIPHER database for recurrent duplications and/or deletions detected across the genome of AFG individuals. From these data, we constructed a chromosome map consisting of SROs and investigated such regions for genes that may be associated with the development of atypical female genitalia. Our study identified 180 unique SROs (7.95 kb to 45.34 Mb) distributed among 22 chromosomes. The most SROs were found in chromosomes X, 17, 11, and 22. None were found in chromosome 3. From these SROs, we identified 22 genes as potential candidates. Although none of these genes are currently associated with AFG, a literature review indicated that almost half were potentially involved in the development and/or function of the reproductive system, and only one gene was associated with a disorder that reported an individual patient with ambiguous genitalia. Our data regarding novel SROs requires further functional investigation to determine the role of the identified candidate genes in the development of atypical female genitalia, and this paper should serve as a catalyst for downstream molecular studies that may eventually affect the genetic counseling, diagnosis, and management of these DSD patients.
Collapse
|
10
|
MAZ regulates chromatin domain insulation and genome architecture. Nat Genet 2022; 54:96-97. [PMID: 35145303 DOI: 10.1038/s41588-021-00995-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
11
|
Ortabozkoyun H, Huang PY, Cho H, Narendra V, LeRoy G, Gonzalez-Buendia E, Skok JA, Tsirigos A, Mazzoni EO, Reinberg D. CRISPR and biochemical screens identify MAZ as a cofactor in CTCF-mediated insulation at Hox clusters. Nat Genet 2022; 54:202-212. [PMID: 35145304 PMCID: PMC8837555 DOI: 10.1038/s41588-021-01008-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 12/22/2021] [Indexed: 12/14/2022]
Abstract
CCCTC-binding factor (CTCF) is critical to three-dimensional genome organization. Upon differentiation, CTCF insulates active and repressed genes within Hox gene clusters. We conducted a genome-wide CRISPR knockout (KO) screen to identify genes required for CTCF-boundary activity at the HoxA cluster, complemented by biochemical approaches. Among the candidates, we identified Myc-associated zinc-finger protein (MAZ) as a cofactor in CTCF insulation. MAZ colocalizes with CTCF at chromatin borders and, similar to CTCF, interacts with the cohesin subunit RAD21. MAZ KO disrupts gene expression and local contacts within topologically associating domains. Similar to CTCF motif deletions, MAZ motif deletions lead to derepression of posterior Hox genes immediately after CTCF boundaries upon differentiation, giving rise to homeotic transformations in mouse. Thus, MAZ is a factor contributing to appropriate insulation, gene expression and genomic architecture during development.
Collapse
Affiliation(s)
- Havva Ortabozkoyun
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Pin-Yao Huang
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Hyunwoo Cho
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA.,Applied Bioinformatics Laboratories, NYU Grossman School of Medicine, New York, NY, USA.,Department of Radiation Oncology, NYU Grossman School of Medicine, New York, NY, USA
| | - Varun Narendra
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gary LeRoy
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Edgar Gonzalez-Buendia
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Jane A Skok
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
| | - Aristotelis Tsirigos
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA.,Applied Bioinformatics Laboratories, NYU Grossman School of Medicine, New York, NY, USA.,Institute for Computational Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | | | - Danny Reinberg
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY, USA. .,Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA.
| |
Collapse
|
12
|
Barratt CLR, Wang C, Baldi E, Toskin I, Kiarie J, Lamb DJ. What advances may the future bring to the diagnosis, treatment, and care of male sexual and reproductive health? Fertil Steril 2022; 117:258-267. [PMID: 35125173 PMCID: PMC8877074 DOI: 10.1016/j.fertnstert.2021.12.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 12/15/2021] [Accepted: 12/15/2021] [Indexed: 12/11/2022]
Abstract
Over the past 40 years, since the publication of the original WHO Laboratory Manual for the Examination and Processing of Human Semen, the laboratory methods used to evaluate semen markedly changed and benefited from improved precision and accuracy, as well as the development of new tests and improved, standardized methodologies. Herein, we present the impact of the changes put forth in the sixth edition together with our views of evolving technologies that may change the methods used for the routine semen analysis, up-and-coming areas for the development of new procedures, and diagnostic approaches that will help to extend the often-descriptive interpretations of several commonly performed semen tests that promise to provide etiologies for the abnormal semen parameters observed. As we look toward the publication of the seventh edition of the manual in approximately 10 years, we describe potential advances that could markedly impact the field of andrology in the future.
Collapse
Affiliation(s)
- Christopher L R Barratt
- Division of Systems Medicine, University of Dundee Medical School, Ninewells Hospital, Dundee, Scotland.
| | - Christina Wang
- Clinical and Translational Science Institute, The Lundquist Institute at Harbor-UCLA Medical Center, Torrance, California
| | - Elisabetta Baldi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Igor Toskin
- Department of Sexual and Reproductive Health and Research, World Health Organization, Geneva, Switzerland
| | - James Kiarie
- Department of Sexual and Reproductive Health and Research, World Health Organization, Geneva, Switzerland
| | - Dolores J Lamb
- The James Buchanan Brady Foundation Department of Urology, Center for Reproductive Genomics and Englander Institute for Personalized Medicine, Weill Cornell Medical College, New York, New York
| |
Collapse
|
13
|
Zheng C, Wu H, Jin S, Li D, Tan S, Zhu X. Roles of Myc-associated zinc finger protein in malignant tumors. Asia Pac J Clin Oncol 2022; 18:506-514. [PMID: 35098656 DOI: 10.1111/ajco.13748] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 12/04/2021] [Indexed: 11/30/2022]
Abstract
As an important transcription factor that is widely expressed in most tissues of the human body, Myc-associated zinc finger protein (MAZ) has been reported highly expressed in many malignant tumors and thought to be a promising therapeutic target for cancer treatment. In this review, we aim to offer a comprehensive understanding of MAZ regulation in malignant tumors. The carboxy terminal of MAZ protein contains six C2H2 zinc fingers, and its regulation of transcription is based on the interaction between the GC-rich DNA binding sites of target genes and its carboxy-terminal zinc finger motifs. MAZ protein has been found to activate or inhibit the transcriptional initiation process of many target genes, as well as play an important role in the transcriptional termination process of some target genes, so MAZ poses dual regulatory functions in the initiation and termination process of gene transcription. Through the transcriptional regulation of c-myc and Ras gene family, MAZ poses an important role in the occurrence and development of breast cancer, pancreatic cancer, prostate cancer, glioblastoma, neuroblastoma, and other malignant tumors. Our review shows a vital role of MAZ in many malignant tumors and provides novel insight for cancer diagnosis and treatment.
Collapse
Affiliation(s)
- Chuanjun Zheng
- Department of Epidemiology and Statistics, School of Public Health, Guilin Medical University, Guilin, China
| | - Hongmei Wu
- Department of Epidemiology and Statistics, School of Public Health, Guilin Medical University, Guilin, China
| | - Song Jin
- Department of Epidemiology and Statistics, School of Public Health, Guilin Medical University, Guilin, China
| | - Di Li
- Department of Epidemiology and Statistics, School of Public Health, Guilin Medical University, Guilin, China
| | - Shengkui Tan
- Department of Epidemiology and Statistics, School of Public Health, Guilin Medical University, Guilin, China
| | - Xiaonian Zhu
- Department of Epidemiology and Statistics, School of Public Health, Guilin Medical University, Guilin, China
| |
Collapse
|
14
|
Punjani N, Kang C, Lamb DJ, Schlegel PN. Current updates and future perspectives in the evaluation of azoospermia: A systematic review. Arab J Urol 2021; 19:206-214. [PMID: 34552771 PMCID: PMC8451618 DOI: 10.1080/2090598x.2021.1954415] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Objectives: To provide a summary of the current evaluation of azoospermia and insights into future perspectives in the evaluation and counselling of men with azoospermia. Methods: A search of PubMed, Cochrane Reviews and Web of Science databases was performed for full-text English-language articles published between 1943 and 2020 focussing on ‘future perspectives’, ‘azoospermia’ and ‘evaluation’. Results: Azoospermia represents a severe form of male infertility characterised by sperm production so impaired that there are no sperm present in the ejaculate. The current evaluation of azoospermia focusses on patient history and physical examination with selected adjunctive laboratory investigations including serum hormones, a karyotype and screening for Y chromosome microdeletions. Future diagnostics are focussed on identifying the underlying genetic aetiologies for azoospermia, as well as a greater emphasis on screening for systemic illness that men with severe infertility may be predisposed to develop. Conclusion: Azoospermia represents an extreme form of male infertility, and evaluation relies heavily on history and physical examination, as genetic evaluations for these individuals remain limited. Future evaluation will focus on next-generation sequencing and more rigorous evaluation for possible co-existing and future risk of systemic disease. ABBREVIATIONS: ADGRG2, adhesion G protein-coupled receptor G2; ASRM: American Society of Reproductive Medicine; AZF: azoospermia factor; CBAVD: congenital bilateral absence of the vas deferens; CFTR: cystic fibrosis transmembrane conductance regulator; CRKL: CRK-like proto-oncogene; E2F1: E2F transcription factor 1; HAUS7: HAUS augmin-like complex subunit 7; HR: hazard ratio; KS: Klinefelter syndrome; MAZ, MYC-associated zinc finger protein; NGS: next-generation sequencing; NOA: non-obstructive azoospermia; OA: obstructive azoospermia; RHOX: reproductive homeobox on the X chromosome; SH2: SRC homology 2; TAF7L: TATA-box binding protein associated factor 7-like; TEX11: testis-expressed 11; WES: whole-exome sequencing
Collapse
Affiliation(s)
- Nahid Punjani
- Department of Urology, Weill Cornell Medical College, New York, NY, USA
| | - Caroline Kang
- Department of Urology, Weill Cornell Medical College, New York, NY, USA
| | - Dolores J Lamb
- Department of Urology, Weill Cornell Medical College, New York, NY, USA.,Englander Institute for Precision Medicine, Weill Cornell Medical College, New York, NY, USA.,Center for Reproductive Genomics, Weill Cornell Medical College, New York, NY, USA
| | - Peter N Schlegel
- Department of Urology, Weill Cornell Medical College, New York, NY, USA.,Center for Reproductive Genomics, Weill Cornell Medical College, New York, NY, USA
| |
Collapse
|
15
|
Identification of the transcription factor MAZ as a regulator of erythropoiesis. Blood Adv 2021; 5:3002-3015. [PMID: 34351390 DOI: 10.1182/bloodadvances.2021004609] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/11/2021] [Indexed: 12/28/2022] Open
Abstract
Erythropoiesis requires a combination of ubiquitous and tissue-specific transcription factors (TFs). Here, through DNA affinity purification followed by mass spectrometry, we have identified the widely expressed protein MAZ (Myc-associated zinc finger) as a TF that binds to the promoter of the erythroid-specific human α-globin gene. Genome-wide mapping in primary human erythroid cells revealed that MAZ also occupies active promoters as well as GATA1-bound enhancer elements of key erythroid genes. Consistent with an important role during erythropoiesis, knockdown of MAZ reduces α-globin expression in K562 cells and impairs differentiation in primary human erythroid cells. Genetic variants in the MAZ locus are associated with changes in clinically important human erythroid traits. Taken together, these findings reveal the zinc-finger TF MAZ to be a previously unrecognized regulator of the erythroid differentiation program.
Collapse
|
16
|
Abstract
Male factor infertility is a common problem. Evidence is emerging regarding the spectrum of systemic disease and illness harbored by infertile men who otherwise appear healthy. In this review, we present evidence that infertile men have poor overall health and increased morbidity and mortality, increased rates of both genitourinary and non-genitourinary malignancy, and greater risks of systemic disease. The review also highlights numerous genetic conditions associated with male infertility as well as emerging translational evidence of genitourinary birth defects and their impact on male infertility. Finally, parallels to the overall health of infertile women are presented. This review highlights the importance of a comprehensive health evaluation of men who present for an infertility assessment.
Collapse
Affiliation(s)
- Nahid Punjani
- James Buchanan Brady Foundation Institute of Urology, Weill Cornell Medical College, New York, NY 10065, USA;
| | - Dolores J Lamb
- James Buchanan Brady Foundation Institute of Urology, Weill Cornell Medical College, New York, NY 10065, USA; .,Englander Institute for Precision Medicine, Weill Cornell Medical College, New York, NY 10021, USA.,Center for Reproductive Genomics, Weill Cornell Medical College, New York, NY 10065, USA
| |
Collapse
|
17
|
Zhou XY, Zheng HY, Han L, Wang Y, Zhang L, Shu XM, Zhang ML, Liu GN, Ding LS. Copy Number Variations Analysis Identifies QPRT as a Candidate Gene Associated With Susceptibility for Solitary Functioning Kidney. Front Genet 2021; 12:575830. [PMID: 34079576 PMCID: PMC8165445 DOI: 10.3389/fgene.2021.575830] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 04/06/2021] [Indexed: 01/03/2023] Open
Abstract
Background The lack of understanding of molecular pathologies of the solitary functioning kidney makes improving and strengthening the continuity of care between pediatric and adult nephrological patients difficult. Copy number variations (CNVs) account for a molecular cause of solitary functioning kidney, but characterization of the pathogenic genes remains challenging. Methods In our prospective cohort study, 99 fetuses clinically diagnosed with a solitary functioning kidney were enrolled and evaluated using chromosomal microarray analysis (CMA). The genetic drivers for the pathogenic CNVs were analyzed. We characterized QPRT localization in fetal kidneys using immunohistochemistry and its expression in adult kidneys using quantitative RT-PCR. Further, QPRT was knocked down using siRNA in human embryonic kidney (HEK293T) cells, and the cell cycle and proliferation were tested. Results Besides one Triple X syndrome and one Down syndrome, we identified a total of 45 CNVs out of 34 subjects. Among the 14 pathogenic CNVs, CNV 16p11.2 reached the highest number of records with the phenotype of kidney anomalies in the Decipher database. Among the 26 genes within the 16p11.2 region, as a key enzyme for nicotinamide adenine dinucleotide (NAD+) biosynthesis, QPRT was distinctly localized in renal tubules but was barely observed in renal interstitial and glomeruli in fetal kidneys. The loss of QPRT prevented cells’ efficient transition into S phase, affected cell-cycle progression, and abrogated proliferation of human embryonic kidney cells. Conclusion Our data suggest that QPRT is a candidate gene associated with susceptibility for solitary functioning kidney. The CNVs discovered in our study exhibit great potential for future applications in genetic counseling and pregnancy management.
Collapse
Affiliation(s)
- Xiao Y Zhou
- Department of Obstetrics, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Hao Y Zheng
- Department of Obstetrics, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Li Han
- Department of Obstetrics, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Yan Wang
- Department of Obstetrics, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Li Zhang
- Department of Obstetrics, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Xiao M Shu
- Department of Obstetrics, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Mu L Zhang
- Department of Obstetrics, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Guan N Liu
- College of Biological and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Lian S Ding
- Department of Neurosurgery, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, China
| |
Collapse
|
18
|
Lopes-Ramos CM, Chen CY, Kuijjer ML, Paulson JN, Sonawane AR, Fagny M, Platig J, Glass K, Quackenbush J, DeMeo DL. Sex Differences in Gene Expression and Regulatory Networks across 29 Human Tissues. Cell Rep 2021; 31:107795. [PMID: 32579922 DOI: 10.1016/j.celrep.2020.107795] [Citation(s) in RCA: 163] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 04/01/2020] [Accepted: 05/29/2020] [Indexed: 11/25/2022] Open
Abstract
Sex differences manifest in many diseases and may drive sex-specific therapeutic responses. To understand the molecular basis of sex differences, we evaluated sex-biased gene regulation by constructing sample-specific gene regulatory networks in 29 human healthy tissues using 8,279 whole-genome expression profiles from the Genotype-Tissue Expression (GTEx) project. We find sex-biased regulatory network structures in each tissue. Even though most transcription factors (TFs) are not differentially expressed between males and females, many have sex-biased regulatory targeting patterns. In each tissue, genes that are differentially targeted by TFs between the sexes are enriched for tissue-related functions and diseases. In brain tissue, for example, genes associated with Parkinson's disease and Alzheimer's disease are targeted by different sets of TFs in each sex. Our systems-based analysis identifies a repertoire of TFs that play important roles in sex-specific architecture of gene regulatory networks, and it underlines sex-specific regulatory processes in both health and disease.
Collapse
Affiliation(s)
| | - Cho-Yi Chen
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
| | - Marieke L Kuijjer
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway
| | - Joseph N Paulson
- Department of Biostatistics, Product Development, Genentech Inc., San Francisco, CA, USA
| | - Abhijeet R Sonawane
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Maud Fagny
- Genetique Quantitative et Evolution-Le Moulon, Universite Paris-Saclay, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - John Platig
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Kimberly Glass
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA; Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - John Quackenbush
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA; Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA.
| |
Collapse
|
19
|
Chen CH, Lin YJ, Lin YY, Lin CH, Feng LY, Chang IYF, Wei KC, Huang CY. Glioblastoma Primary Cells Retain the Most Copy Number Alterations That Predict Poor Survival in Glioma Patients. Front Oncol 2021; 11:621432. [PMID: 33981597 PMCID: PMC8108987 DOI: 10.3389/fonc.2021.621432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 04/06/2021] [Indexed: 11/16/2022] Open
Abstract
Gliomas are solid tumors that originate from glial cells in the brain or spine and account for 74.6% of malignant primary central nervous system tumors worldwide. As patient-derived primary cells are important tools for drug screening and new therapy development in glioma, we aim to understand the genomic similarity of the primary cells to their parental tumors by comparing their whole-genome copy number variations and expression profile of glioma clinicopathologic factors. We found that the primary cells from grade II/III gliomas lost most of the gene copy number alterations (CNAs), which were mainly located on chromosome 1p and 19q in their parental tumors. The glioblastoma (GBM) primary cells preserved 83.7% of the gene CNAs in the parental GBM tumors, including chromosome 7 gain and 10q loss. The CNA gains of LINC00226 and ADAM6 and the chromosome 16p11 loss were reconstituted in primary cells from both grade II/III gliomas and GBMs. Interestingly, we found these CNAs were correlated to overall survival (OS) in glioma patients using the Merged Cohort LGG and GBM dataset from cBioPortal. The gene CNAs preserved in glioma primary cells often predicted poor survival, whereas the gene CNAs lost in grade II/III primary cells were mainly associated to better prognosis in glioma patients. Glioma prognostic factors that predict better survival, such as IDH mutations and 1p/19q codeletion in grade II/III gliomas, were lost in their primary cells, whereas methylated MGMT promoters as well as TERT promoter mutations were preserved in GBM primary cells while lost in grade II/III primary cells. Our results suggest that GBM primary cells tend to preserve CNAs in their parental tumors, and these CNAs are correlated to poor OS and predict worse prognosis in glioma patients.
Collapse
Affiliation(s)
- Chia-Hua Chen
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Department of Neurosurgery, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Ya-Jui Lin
- Department of Neurosurgery, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan.,The Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
| | - You-Yu Lin
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chang-Hung Lin
- Department of Neurosurgery, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan.,Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Li-Ying Feng
- School of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Neurosurgery, New Taipei Municipal TuCheng Hospital, New Taipei City, Taiwan
| | - Ian Yi-Feng Chang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Department of Neurosurgery, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Kuo-Chen Wei
- Department of Neurosurgery, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan.,School of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Neurosurgery, New Taipei Municipal TuCheng Hospital, New Taipei City, Taiwan
| | - Chiung-Yin Huang
- School of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Neurosurgery, New Taipei Municipal TuCheng Hospital, New Taipei City, Taiwan
| |
Collapse
|
20
|
Verbitsky M, Krithivasan P, Batourina E, Khan A, Graham SE, Marasà M, Kim H, Lim TY, Weng PL, Sánchez-Rodríguez E, Mitrotti A, Ahram DF, Zanoni F, Fasel DA, Westland R, Sampson MG, Zhang JY, Bodria M, Kil BH, Shril S, Gesualdo L, Torri F, Scolari F, Izzi C, van Wijk JA, Saraga M, Santoro D, Conti G, Barton DE, Dobson MG, Puri P, Furth SL, Warady BA, Pisani I, Fiaccadori E, Allegri L, Degl'Innocenti ML, Piaggio G, Alam S, Gigante M, Zaza G, Esposito P, Lin F, Simões-e-Silva AC, Brodkiewicz A, Drozdz D, Zachwieja K, Miklaszewska M, Szczepanska M, Adamczyk P, Tkaczyk M, Tomczyk D, Sikora P, Mizerska-Wasiak M, Krzemien G, Szmigielska A, Zaniew M, Lozanovski VJ, Gucev Z, Ionita-Laza I, Stanaway IB, Crosslin DR, Wong CS, Hildebrandt F, Barasch J, Kenny EE, Loos RJ, Levy B, Ghiggeri GM, Hakonarson H, Latos-Bieleńska A, Materna-Kiryluk A, Darlow JM, Tasic V, Willer C, Kiryluk K, Sanna-Cherchi S, Mendelsohn CL, Gharavi AG. Copy Number Variant Analysis and Genome-wide Association Study Identify Loci with Large Effect for Vesicoureteral Reflux. J Am Soc Nephrol 2021; 32:805-820. [PMID: 33597122 PMCID: PMC8017540 DOI: 10.1681/asn.2020050681] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 12/04/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Vesicoureteral reflux (VUR) is a common, familial genitourinary disorder, and a major cause of pediatric urinary tract infection (UTI) and kidney failure. The genetic basis of VUR is not well understood. METHODS A diagnostic analysis sought rare, pathogenic copy number variant (CNV) disorders among 1737 patients with VUR. A GWAS was performed in 1395 patients and 5366 controls, of European ancestry. RESULTS Altogether, 3% of VUR patients harbored an undiagnosed rare CNV disorder, such as the 1q21.1, 16p11.2, 22q11.21, and triple X syndromes ((OR, 3.12; 95% CI, 2.10 to 4.54; P=6.35×10-8) The GWAS identified three study-wide significant and five suggestive loci with large effects (ORs, 1.41-6.9), containing canonical developmental genes expressed in the developing urinary tract (WDPCP, OTX1, BMP5, VANGL1, and WNT5A). In particular, 3.3% of VUR patients were homozygous for an intronic variant in WDPCP (rs13013890; OR, 3.65; 95% CI, 2.39 to 5.56; P=1.86×10-9). This locus was associated with multiple genitourinary phenotypes in the UK Biobank and eMERGE studies. Analysis of Wnt5a mutant mice confirmed the role of Wnt5a signaling in bladder and ureteric morphogenesis. CONCLUSIONS These data demonstrate the genetic heterogeneity of VUR. Altogether, 6% of patients with VUR harbored a rare CNV or a common variant genotype conferring an OR >3. Identification of these genetic risk factors has multiple implications for clinical care and for analysis of outcomes in VUR.
Collapse
Affiliation(s)
- Miguel Verbitsky
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Priya Krithivasan
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | | | - Atlas Khan
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Sarah E. Graham
- Department of Internal Medicine, Cardiology, University of Michigan, Ann Arbor, Michigan
| | - Maddalena Marasà
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Hyunwoo Kim
- Department of Urology, Columbia University, New York, New York
| | - Tze Y. Lim
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Patricia L. Weng
- Department of Pediatric Nephrology, University of California, Los Angeles Medical Center and University of California, Los Angeles Medical Center-Santa Monica, Los Angeles, California
| | | | - Adele Mitrotti
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
- Section of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Dina F. Ahram
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Francesca Zanoni
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - David A. Fasel
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Rik Westland
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
- Department of Pediatric Nephrology, Vrije Universiteit University Medical Center, Amsterdam, The Netherlands
| | - Matthew G. Sampson
- Division of Nephrology, Boston Children’s Hospital, Boston, Massachusetts
| | - Jun Y. Zhang
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Monica Bodria
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Byum Hee Kil
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Shirlee Shril
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Loreto Gesualdo
- Section of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Fabio Torri
- Department of Pediatric Surgery, Spedali Civili Children’s Hospital of Brescia, Brescia, Italy
| | - Francesco Scolari
- Chair and Division of Nephrology, University and Spedali Civili Hospital, Brescia, Italy
| | - Claudia Izzi
- Division of Nephrology and Department of Obstetrics and Gynecology, ASST Spedali Civili of Brescia, Brescia, Italy
| | - Joanna A.E. van Wijk
- Department of Pediatric Nephrology, Vrije Universiteit University Medical Center, Amsterdam, The Netherlands
| | - Marijan Saraga
- Department of Pediatrics, University Hospital of Split, Split, Croatia
- School of Medicine, University of Split, Split, Croatia
| | - Domenico Santoro
- Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | - Giovanni Conti
- Department of Pediatric Nephrology, Azienda Ospedaliera Universitaria “G. Martino,” Messina, Italy
| | - David E. Barton
- University College Dublin School of Medicine, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
- Department of Clinical Genetics, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
| | - Mark G. Dobson
- Department of Clinical Genetics, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
- National Children’s Research Centre, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
| | - Prem Puri
- National Children’s Research Centre, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
- Department of Pediatric Surgery, Beacon Hospital, University College Dublin, Dublin, Ireland
| | - Susan L. Furth
- Division of Nephrology, Departments of Pediatrics and Epidemiology, Perelman School of Medicine at the University of Pennsylvania, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Bradley A. Warady
- Division of Nephrology, Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Children’s Mercy Kansas City, Kansas City, Missouri
| | - Isabella Pisani
- Nephrology Unit, Parma University Hospital and Department of Medicine and Surgery, Parma University Medical School, Parma, Italy
| | - Enrico Fiaccadori
- Nephrology Unit, Parma University Hospital and Department of Medicine and Surgery, Parma University Medical School, Parma, Italy
| | - Landino Allegri
- Nephrology Unit, Parma University Hospital and Department of Medicine and Surgery, Parma University Medical School, Parma, Italy
| | - Maria Ludovica Degl'Innocenti
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Giorgio Piaggio
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Shumyle Alam
- Department of Pediatric Urology, Columbia University College of Physicians and Surgeons, New York, New York
| | - Maddalena Gigante
- Section of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Gianluigi Zaza
- Renal and Dialysis Unit, Department of Medicine, School of Medicine, University of Verona, Verona, Italy
| | - Pasquale Esposito
- Department of Internal Medicine, Nephrology, Dialysis and Transplantation Clinics, Genoa University and IRCCS Policlinico San Martino, Genova, Italy
| | - Fangming Lin
- Division of Pediatric Nephrology, Department of Pediatrics, Columbia University, New York, New York
| | - Ana Cristina Simões-e-Silva
- Department of Pediatrics, Unit of Pediatric Nephrology, Interdisciplinary Laboratory of Medical Investigation, Faculty of Medicine, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Andrzej Brodkiewicz
- Department of Pediatrics, Child Nephrology, Dialysotheraphy and Management of Acute Poisoning, Pomeranian Medical University, Szczecin, Poland
| | - Dorota Drozdz
- Department of Pediatric Nephrology and Hypertension, Jagiellonian University Medical College, Krakow, Poland
| | - Katarzyna Zachwieja
- Department of Pediatric Nephrology and Hypertension, Jagiellonian University Medical College, Krakow, Poland
| | - Monika Miklaszewska
- Department of Pediatric Nephrology and Hypertension, Jagiellonian University Medical College, Krakow, Poland
| | - Maria Szczepanska
- Department of Pediatrics, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, Katowice, Poland
| | - Piotr Adamczyk
- Department of Pediatrics, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, Katowice, Poland
| | - Marcin Tkaczyk
- Department of Pediatrics, Immunology and Nephrology, Polish Mother’s Memorial Hospital Research Institute, Lodz, Poland
| | - Daria Tomczyk
- Department of Pediatrics, Immunology and Nephrology, Polish Mother’s Memorial Hospital Research Institute, Lodz, Poland
| | - Przemyslaw Sikora
- Department of Pediatric Nephrology, Medical University of Lublin, Lublin, Poland
| | | | - Grazyna Krzemien
- Department of Pediatrics and Nephrology, Medical University of Warsaw, Poland
| | | | - Marcin Zaniew
- Department of Pediatrics, University of Zielona Góra, Zielona Góra, Poland
| | - Vladimir J. Lozanovski
- University Clinic for General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
- University Children’s Hospital, Medical Faculty of Skopje, Skopje, Macedonia
| | - Zoran Gucev
- University Children’s Hospital, Medical Faculty of Skopje, Skopje, Macedonia
| | | | - Ian B. Stanaway
- Department of Biomedical Informatics and Medical Education, University of Washington School of Medicine, Seattle, Washington
| | - David R. Crosslin
- Department of Biomedical Informatics and Medical Education, University of Washington School of Medicine, Seattle, Washington
| | - Craig S. Wong
- Division of Pediatric Nephrology, University of New Mexico Children’s Hospital, Albuquerque, New Mexico
| | - Friedhelm Hildebrandt
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jonathan Barasch
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
- Department of Urology, Columbia University, New York, New York
| | - Eimear E. Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ruth J.F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York
| | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University, New York, New York
| | - Gian Marco Ghiggeri
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children’s Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Anna Latos-Bieleńska
- Department of Medical Genetics, Poznan University of Medical Sciences, and NZOZ Center for Medical Genetics GENESIS, Poznan, Poland
| | - Anna Materna-Kiryluk
- Department of Medical Genetics, Poznan University of Medical Sciences, and NZOZ Center for Medical Genetics GENESIS, Poznan, Poland
| | - John M. Darlow
- Department of Clinical Genetics, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
- National Children’s Research Centre, Our Lady’s Children’s Hospital Crumlin, Dublin, Ireland
| | - Velibor Tasic
- University Children’s Hospital, Medical Faculty of Skopje, Skopje, Macedonia
| | - Cristen Willer
- Department of Internal Medicine, Cardiology, University of Michigan, Ann Arbor, Michigan
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan
- Department of Computational Medicine and Bioinformatics, Ann Arbor, Michigan
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Simone Sanna-Cherchi
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | | | - Ali G. Gharavi
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| |
Collapse
|
21
|
Xiao T, Li X, Felsenfeld G. The Myc-associated zinc finger protein (MAZ) works together with CTCF to control cohesin positioning and genome organization. Proc Natl Acad Sci U S A 2021; 118:e2023127118. [PMID: 33558242 PMCID: PMC7896315 DOI: 10.1073/pnas.2023127118] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The Myc-associated zinc finger protein (MAZ) is often found at genomic binding sites adjacent to CTCF, a protein which affects large-scale genome organization through its interaction with cohesin. We show here that, like CTCF, MAZ physically interacts with a cohesin subunit and can arrest cohesin sliding independently of CTCF. It also shares with CTCF the ability to independently pause the elongating form of RNA polymerase II, and consequently affects RNA alternative splicing. CTCF/MAZ double sites are more effective at sequestering cohesin than sites occupied only by CTCF. Furthermore, depletion of CTCF results in preferential loss of CTCF from sites not occupied by MAZ. In an assay for insulation activity like that used for CTCF, binding of MAZ to sites between an enhancer and promoter results in down-regulation of reporter gene expression, supporting a role for MAZ as an insulator protein. Hi-C analysis of the effect of MAZ depletion on genome organization shows that local interactions within topologically associated domains (TADs) are disrupted, as well as contacts that establish the boundaries of individual TADs. We conclude that MAZ augments the action of CTCF in organizing the genome, but also shares properties with CTCF that allow it to act independently.
Collapse
Affiliation(s)
- Tiaojiang Xiao
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892-0540
| | - Xin Li
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892-0540
| | - Gary Felsenfeld
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892-0540
| |
Collapse
|
22
|
Westland R, Renkema KY, Knoers NV. Clinical Integration of Genome Diagnostics for Congenital Anomalies of the Kidney and Urinary Tract. Clin J Am Soc Nephrol 2021; 16:128-137. [PMID: 32312792 PMCID: PMC7792653 DOI: 10.2215/cjn.14661119] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Revolutions in genetics, epigenetics, and bioinformatics are currently changing the outline of diagnostics and clinical medicine. From a nephrologist's perspective, individuals with congenital anomalies of the kidney and urinary tract (CAKUT) are an important patient category: not only is CAKUT the predominant cause of kidney failure in children and young adults, but the strong phenotypic and genotypic heterogeneity of kidney and urinary tract malformations has hampered standardization of clinical decision making until now. However, patients with CAKUT may benefit from precision medicine, including an integrated diagnostics trajectory, genetic counseling, and personalized management to improve clinical outcomes of developmental kidney and urinary tract defects. In this review, we discuss the present understanding of the molecular etiology of CAKUT and the currently available genome diagnostic modalities in the clinical care of patients with CAKUT. Finally, we discuss how clinical integration of findings from large-scale genetic, epigenetic, and gene-environment interaction studies may improve the prognosis of all individuals with CAKUT.
Collapse
Affiliation(s)
- Rik Westland
- Department of Pediatric Nephrology, Amsterdam UMC, Amsterdam, The Netherlands
| | - Kirsten Y. Renkema
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Nine V.A.M. Knoers
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands,Department of Genetics, University Medical Centre Groningen, Groningen, The Netherlands
| |
Collapse
|
23
|
Medina-Martinez O, Haller M, Rosenfeld JA, O'Neill MA, Lamb DJ, Jamrich M. The transcription factor Maz is essential for normal eye development. Dis Model Mech 2020; 13:dmm044412. [PMID: 32571845 PMCID: PMC7449797 DOI: 10.1242/dmm.044412] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 06/10/2020] [Indexed: 12/19/2022] Open
Abstract
Wnt/β-catenin signaling has an essential role in eye development. Faulty regulation of this pathway results in ocular malformations, owing to defects in cell-fate determination and differentiation. Herein, we show that disruption of Maz, the gene encoding Myc-associated zinc-finger transcription factor, produces developmental eye defects in mice and humans. Expression of key genes involved in the Wnt cascade, Sfrp2, Wnt2b and Fzd4, was significantly increased in mice with targeted inactivation of Maz, resulting in abnormal peripheral eye formation with reduced proliferation of the progenitor cells in the region. Paradoxically, the Wnt reporter TCF-Lef1 displayed a significant downregulation in Maz-deficient eyes. Molecular analysis indicates that Maz is necessary for the activation of the Wnt/β-catenin pathway and participates in the network controlling ciliary margin patterning. Copy-number variations and single-nucleotide variants of MAZ were identified in humans that result in abnormal ocular development. The data support MAZ as a key contributor to the eye comorbidities associated with chromosome 16p11.2 copy-number variants and as a transcriptional regulator of ocular development.
Collapse
Affiliation(s)
- Olga Medina-Martinez
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Meade Haller
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Reproductive Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jill A Rosenfeld
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Baylor Genetics Laboratories, Houston, TX 77021, USA
| | - Marisol A O'Neill
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Reproductive Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dolores J Lamb
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Reproductive Medicine, Baylor College of Medicine, Houston, TX 77030, USA
- James Buchanan Brady Foundation Department of Urology, Weill Cornell Medical College, New York City, NY 10065, USA
- Englander Institute for Precision Medicine, Weill Cornell Medical College, New York City, NY 10065, USA
- Center for Reproductive Genomics, Weill Cornell Medical College, New York City, NY 10065, USA
| | - Milan Jamrich
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| |
Collapse
|
24
|
Punjani N, Lamb DJ. Male infertility and genitourinary birth defects: there is more than meets the eye. Fertil Steril 2020; 114:209-218. [PMID: 32741459 PMCID: PMC10590568 DOI: 10.1016/j.fertnstert.2020.06.042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 06/24/2020] [Accepted: 06/24/2020] [Indexed: 12/17/2022]
Abstract
Male factor infertility is a significant problem present in up to 50% of infertile couples. The relationship between male infertility and systemic disease is of significant interest, and emerging evidence suggests a relationship between male infertility and male genitourinary (GU) birth defects (cryptorchidism, hypospadias, ambiguous genitalia, and congenital anomalies of the kidney and urinary tract). Many of these birth defects are treated in isolation by busy urologists without acknowledgment that these may be related to more global syndromic conditions. Conversely, geneticists and nonurologists who treat variable systemic phenotypes may overlook GU defects, which are indeed related conditions. Many of these defects are attributed to copy number variants dosage-sensitive genes due to chromosome microdeletions or microduplications. These variants are responsible for disease phenotypes seen in the general population. The copy number variants described in this review are syndromic in some cases and responsible for both GU birth defects as well as other systemic phenotypes. This review highlights the emerging evidence between these birth defects, male infertility, and other systemic conditions.
Collapse
Affiliation(s)
- Nahid Punjani
- James Buchanan Brady Foundation Institute of Urology, Weill Cornell Medical College, New York, New York
| | - Dolores J Lamb
- James Buchanan Brady Foundation Institute of Urology, Weill Cornell Medical College, New York, New York; Englander Institute for Precision Medicine, Weill Cornell Medical College, New York, New York; Center for Reproductive Genomics, Weill Cornell Medical College, New York, New York.
| |
Collapse
|
25
|
Yusuff T, Jensen M, Yennawar S, Pizzo L, Karthikeyan S, Gould DJ, Sarker A, Gedvilaite E, Matsui Y, Iyer J, Lai ZC, Girirajan S. Drosophila models of pathogenic copy-number variant genes show global and non-neuronal defects during development. PLoS Genet 2020; 16:e1008792. [PMID: 32579612 PMCID: PMC7313740 DOI: 10.1371/journal.pgen.1008792] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 04/23/2020] [Indexed: 11/25/2022] Open
Abstract
While rare pathogenic copy-number variants (CNVs) are associated with both neuronal and non-neuronal phenotypes, functional studies evaluating these regions have focused on the molecular basis of neuronal defects. We report a systematic functional analysis of non-neuronal defects for homologs of 59 genes within ten pathogenic CNVs and 20 neurodevelopmental genes in Drosophila melanogaster. Using wing-specific knockdown of 136 RNA interference lines, we identified qualitative and quantitative phenotypes in 72/79 homologs, including 21 lines with severe wing defects and six lines with lethality. In fact, we found that 10/31 homologs of CNV genes also showed complete or partial lethality at larval or pupal stages with ubiquitous knockdown. Comparisons between eye and wing-specific knockdown of 37/45 homologs showed both neuronal and non-neuronal defects, but with no correlation in the severity of defects. We further observed disruptions in cell proliferation and apoptosis in larval wing discs for 23/27 homologs, and altered Wnt, Hedgehog and Notch signaling for 9/14 homologs, including AATF/Aatf, PPP4C/Pp4-19C, and KIF11/Klp61F. These findings were further supported by tissue-specific differences in expression patterns of human CNV genes, as well as connectivity of CNV genes to signaling pathway genes in brain, heart and kidney-specific networks. Our findings suggest that multiple genes within each CNV differentially affect both global and tissue-specific developmental processes within conserved pathways, and that their roles are not restricted to neuronal functions. Rare copy-number variants (CNVs), or large deletions and duplications in the genome, are associated with both neuronal and non-neuronal clinical features. Previous functional studies for these disorders have primarily focused on understanding the cellular mechanisms for neurological and behavioral phenotypes. To understand how genes within these CNVs contribute to developmental defects in non-neuronal tissues, we assessed 79 homologs of CNV and known neurodevelopmental genes in Drosophila models. We found that most homologs showed developmental defects when knocked down in the adult fly wing, ranging from mild size changes to severe wrinkled wings or lethality. Although a majority of tested homologs showed defects when knocked down specifically in wings or eyes, we found no correlation in the severity of the observed defects in these two tissues. A subset of the homologs showed disruptions in cellular processes in the developing fly wing, including alterations in cell proliferation, apoptosis, and cellular signaling pathways. Furthermore, human CNV genes also showed differences in gene expression patterns and interactions with signaling pathway genes across multiple human tissues. Our findings suggest that genes within CNV disorders affect global developmental processes in both neuronal and non-neuronal tissues.
Collapse
Affiliation(s)
- Tanzeen Yusuff
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Matthew Jensen
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Sneha Yennawar
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Lucilla Pizzo
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Siddharth Karthikeyan
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Dagny J. Gould
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Avik Sarker
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Erika Gedvilaite
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Yurika Matsui
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Janani Iyer
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Zhi-Chun Lai
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Santhosh Girirajan
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania, United States of America
- * E-mail:
| |
Collapse
|
26
|
Human and mouse studies establish TBX6 in Mendelian CAKUT and as a potential driver of kidney defects associated with the 16p11.2 microdeletion syndrome. Kidney Int 2020; 98:1020-1030. [PMID: 32450157 DOI: 10.1016/j.kint.2020.04.045] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 03/03/2020] [Accepted: 04/09/2020] [Indexed: 12/22/2022]
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUTs) are the most common cause of chronic kidney disease in children. Human 16p11.2 deletions have been associated with CAKUT, but the responsible molecular mechanism remains to be illuminated. To explore this, we investigated 102 carriers of 16p11.2 deletion from multi-center cohorts, among which we retrospectively ascertained kidney morphologic and functional data from 37 individuals (12 Chinese and 25 Caucasian/Hispanic). Significantly higher CAKUT rates were observed in 16p11.2 deletion carriers (about 25% in Chinese and 16% in Caucasian/Hispanic) than those found in the non-clinically ascertained general populations (about 1/1000 found at autopsy). Furthermore, we identified seven additional individuals with heterozygous loss-of-function variants in TBX6, a gene that maps to the 16p11.2 region. Four of these seven cases showed obvious CAKUT. To further investigate the role of TBX6 in kidney development, we engineered mice with mutated Tbx6 alleles. The Tbx6 heterozygous null (i.e., loss-of-function) mutant (Tbx6+/‒) resulted in 13% solitary kidneys. Remarkably, this incidence increased to 29% in a compound heterozygous model (Tbx6mh/‒) that reduced Tbx6 gene dosage to below haploinsufficiency, by combining the null allele with a novel mild hypomorphic allele (mh). Renal hypoplasia was also frequently observed in these Tbx6-mutated mouse models. Thus, our findings in patients and mice establish TBX6 as a novel gene involved in CAKUT and its gene dosage insufficiency as a potential driver for kidney defects observed in the 16p11.2 microdeletion syndrome.
Collapse
|
27
|
Increased gene copy number of DEFA1/DEFA3 worsens sepsis by inducing endothelial pyroptosis. Proc Natl Acad Sci U S A 2019; 116:3161-3170. [PMID: 30718392 PMCID: PMC6386704 DOI: 10.1073/pnas.1812947116] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Sepsis claims an estimated 30 million episodes and 6 million deaths per year, and treatment options are rather limited. Human neutrophil peptides 1-3 (HNP1-3) are the most abundant neutrophil granule proteins but their neutrophil content varies because of unusually extensive gene copy number polymorphism. A genetic association study found that increased copy number of the HNP-encoding gene DEFA1/DEFA3 is a risk factor for organ dysfunction during sepsis development. However, direct experimental evidence demonstrating that these risk alleles are pathogenic for sepsis is lacking because the genes are present only in some primates and humans. Here, we generate DEFA1/DEFA3 transgenic mice with neutrophil-specific expression of the peptides. We show that mice with high copy number of DEFA1/DEFA3 genes have more severe sepsis-related vital organ damage and mortality than mice with low copy number of DEFA1/DEFA3 or wild-type mice, resulting from more severe endothelial barrier dysfunction and endothelial cell pyroptosis after sepsis challenge. Mechanistically, HNP-1 induces endothelial cell pyroptosis via P2X7 receptor-mediating canonical caspase-1 activation in a NLRP3 inflammasome-dependent manner. Based on these findings, we engineered a monoclonal antibody against HNP-1 to block the interaction with P2X7 and found that the blocking antibody protected mice carrying high copy number of DEFA1/DEFA3 from lethal sepsis. We thus demonstrate that DEFA1/DEFA3 copy number variation strongly modulates sepsis development in vivo and explore a paradigm for the precision treatment of sepsis tailored by individual genetic information.
Collapse
|
28
|
Abstract
Variably expressive copy-number variants (CNVs) are characterized by extensive phenotypic heterogeneity of neuropsychiatric phenotypes. Approaches to identify single causative genes for these phenotypes within each CNV have not been successful. Here, we posit using multiple lines of evidence, including pathogenicity metrics, functional assays of model organisms, and gene expression data, that multiple genes within each CNV region are likely responsible for the observed phenotypes. We propose that candidate genes within each region likely interact with each other through shared pathways to modulate the individual gene phenotypes, emphasizing the genetic complexity of CNV-associated neuropsychiatric features.
Collapse
Affiliation(s)
- Matthew Jensen
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Bioinformatics and Genomics Program, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Santhosh Girirajan
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Bioinformatics and Genomics Program, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| |
Collapse
|
29
|
Iyer J, Singh MD, Jensen M, Patel P, Pizzo L, Huber E, Koerselman H, Weiner AT, Lepanto P, Vadodaria K, Kubina A, Wang Q, Talbert A, Yennawar S, Badano J, Manak JR, Rolls MM, Krishnan A, Girirajan S. Pervasive genetic interactions modulate neurodevelopmental defects of the autism-associated 16p11.2 deletion in Drosophila melanogaster. Nat Commun 2018; 9:2548. [PMID: 29959322 PMCID: PMC6026208 DOI: 10.1038/s41467-018-04882-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 05/22/2018] [Indexed: 12/26/2022] Open
Abstract
As opposed to syndromic CNVs caused by single genes, extensive phenotypic heterogeneity in variably-expressive CNVs complicates disease gene discovery and functional evaluation. Here, we propose a complex interaction model for pathogenicity of the autism-associated 16p11.2 deletion, where CNV genes interact with each other in conserved pathways to modulate expression of the phenotype. Using multiple quantitative methods in Drosophila RNAi lines, we identify a range of neurodevelopmental phenotypes for knockdown of individual 16p11.2 homologs in different tissues. We test 565 pairwise knockdowns in the developing eye, and identify 24 interactions between pairs of 16p11.2 homologs and 46 interactions between 16p11.2 homologs and neurodevelopmental genes that suppress or enhance cell proliferation phenotypes compared to one-hit knockdowns. These interactions within cell proliferation pathways are also enriched in a human brain-specific network, providing translational relevance in humans. Our study indicates a role for pervasive genetic interactions within CNVs towards cellular and developmental phenotypes. The 16p11.2 deletion leads to a range of neurodevelopmental phenotypes, but to date, sequencing studies have not been able to pinpoint individual genes that are causative for the disease on their own. Here, using Drosophila homologs of 14 16p11.2 genes, the authors take a combinatorial approach to show that gene interactions contribute to a neurological phenotype.
Collapse
Affiliation(s)
- Janani Iyer
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Mayanglambam Dhruba Singh
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Matthew Jensen
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA.,Bioinformatics and Genomics Program, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Payal Patel
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Lucilla Pizzo
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Emily Huber
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Haley Koerselman
- Department of Biology, University of Iowa, Iowa City, IA, 52242, USA
| | - Alexis T Weiner
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Paola Lepanto
- Human Molecular Genetics Laboratory, Institut Pasteur de Montevideo, Montevideo, CP11400, Uruguay
| | - Komal Vadodaria
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Alexis Kubina
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Qingyu Wang
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA.,Bioinformatics and Genomics Program, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Abigail Talbert
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Sneha Yennawar
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Jose Badano
- Human Molecular Genetics Laboratory, Institut Pasteur de Montevideo, Montevideo, CP11400, Uruguay
| | - J Robert Manak
- Department of Biology, University of Iowa, Iowa City, IA, 52242, USA.,Department of Pediatrics, University of Iowa, Iowa City, IA, 52242, USA
| | - Melissa M Rolls
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Arjun Krishnan
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI, 48824, USA.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Santhosh Girirajan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA. .,Bioinformatics and Genomics Program, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA. .,Department of Anthropology, The Pennsylvania State University, University Park, PA, 16802, USA.
| |
Collapse
|
30
|
|