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Lin J, Carman PJ, Gambogi CW, Kendsersky NM, Chuang E, Gates SN, Yokom AL, Rizo AN, Southworth DR, Shorter J. Design principles to tailor Hsp104 therapeutics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.26.591398. [PMID: 38712168 PMCID: PMC11071516 DOI: 10.1101/2024.04.26.591398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The hexameric AAA+ disaggregase, Hsp104, collaborates with Hsp70 and Hsp40 via its autoregulatory middle domain (MD) to solubilize aggregated protein conformers. However, how ATP- or ADP-specific MD configurations regulate Hsp104 hexamers remains poorly understood. Here, we define an ATP-specific network of interprotomer contacts between nucleotide-binding domain 1 (NBD1) and MD helix L1, which tunes Hsp70 collaboration. Manipulating this network can: (a) reduce Hsp70 collaboration without enhancing activity; (b) generate Hsp104 hypomorphs that collaborate selectively with class B Hsp40s; (c) produce Hsp70-independent potentiated variants; or (d) create species barriers between Hsp104 and Hsp70. Conversely, ADP-specific intraprotomer contacts between MD helix L2 and NBD1 restrict activity, and their perturbation frequently potentiates Hsp104. Importantly, adjusting the NBD1:MD helix L1 rheostat via rational design enables finely tuned collaboration with Hsp70 to safely potentiate Hsp104, minimize off-target toxicity, and counteract FUS proteinopathy in human cells. Thus, we establish important design principles to tailor Hsp104 therapeutics.
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Affiliation(s)
- JiaBei Lin
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
| | - Peter J. Carman
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
| | - Craig W. Gambogi
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
| | - Nathan M. Kendsersky
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
- Pharmacology Graduate Group Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
| | - Edward Chuang
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
- Pharmacology Graduate Group Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
| | - Stephanie N. Gates
- Graduate Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109. U.S.A
- Current address: Department of Biochemistry, University of Missouri, Columbia, MO 65211. U.S.A
| | - Adam L. Yokom
- Graduate Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109. U.S.A
- Current address: Department of Biochemistry, University of Missouri, Columbia, MO 65211. U.S.A
| | - Alexandrea N. Rizo
- Graduate Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109. U.S.A
| | - Daniel R. Southworth
- Department of Biochemistry and Biophysics and the Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA 94158. U.S.A
| | - James Shorter
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
- Pharmacology Graduate Group Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
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Parisi X, Bledsoe JR. Discerning clinicopathological features of congenital neutropenia syndromes: an approach to diagnostically challenging differential diagnoses. J Clin Pathol 2024:jcp-2022-208686. [PMID: 38589208 DOI: 10.1136/jcp-2022-208686] [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: 01/18/2024] [Accepted: 03/28/2024] [Indexed: 04/10/2024]
Abstract
The congenital neutropenia syndromes are rare haematological conditions defined by impaired myeloid precursor differentiation or function. Patients are prone to severe infections with high mortality rates in early life. While some patients benefit from granulocyte colony-stimulating factor treatment, they may still face an increased risk of bone marrow failure, myelodysplastic syndrome and acute leukaemia. Accurate diagnosis is crucial for improved outcomes; however, diagnosis depends on familiarity with a heterogeneous group of rare disorders that remain incompletely characterised. The clinical and pathological overlap between reactive conditions, primary and congenital neutropenias, bone marrow failure, and myelodysplastic syndromes further clouds diagnostic clarity.We review the diagnostically useful clinicopathological and morphological features of reactive causes of neutropenia and the most common primary neutropenia disorders: constitutional/benign ethnic neutropenia, chronic idiopathic neutropenia, cyclic neutropenia, severe congenital neutropenia (due to mutations in ELANE, GFI1, HAX1, G6PC3, VPS45, JAGN1, CSF3R, SRP54, CLPB and WAS), GATA2 deficiency, Warts, hypogammaglobulinaemia, infections and myelokathexis syndrome, Shwachman-Diamond Syndrome, the lysosomal storage disorders with neutropenia: Chediak-Higashi, Hermansky-Pudlak, and Griscelli syndromes, Cohen, and Barth syndromes. We also detail characteristic cytogenetic and molecular factors at diagnosis and in progression to myelodysplastic syndrome/leukaemia.
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Affiliation(s)
- Xenia Parisi
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jacob R Bledsoe
- Department of Pathology, Boston Children's Hospital, Boston, Massachusetts, USA
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3
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Oyarbide U, Crane GM, Corey SJ. The metabolic basis of inherited neutropenias. Br J Haematol 2024; 204:45-55. [PMID: 38049194 DOI: 10.1111/bjh.19192] [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: 08/29/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 12/06/2023]
Abstract
Neutrophils are the shortest-lived blood cells, which requires a prodigious degree of proliferation and differentiation to sustain physiologically sufficient numbers and be poised to respond quickly to infectious emergencies. More than 107 neutrophils are produced every minute in an adult bone marrow-a process that is tightly regulated by a small group of cytokines and chemical mediators and dependent on nutrients and energy. Like granulocyte colony-stimulating factor, the primary growth factor for granulopoiesis, they stimulate signalling pathways, some affecting metabolism. Nutrient or energy deficiency stresses the survival, proliferation, and differentiation of neutrophils and their precursors. Thus, it is not surprising that monogenic disorders related to metabolism exist that result in neutropenia. Among these are pathogenic mutations in HAX1, G6PC3, SLC37A4, TAFAZZIN, SBDS, EFL1 and the mitochondrial disorders. These mutations perturb carbohydrate, lipid and/or protein metabolism. We hypothesize that metabolic disturbances may drive the pathogenesis of a subset of inherited neutropenias just as defects in DNA damage response do in Fanconi anaemia, telomere maintenance in dyskeratosis congenita and ribosome formation in Diamond-Blackfan anaemia. Greater understanding of metabolic pathways in granulopoiesis will identify points of vulnerability in production and may point to new strategies for the treatment of neutropenias.
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Affiliation(s)
- Usua Oyarbide
- Department of Cancer Biology, Cleveland Clinic, Cleveland, Ohio, USA
- Department of Pediatrics, Cleveland Clinic, Cleveland, Ohio, USA
| | - Genevieve M Crane
- Department of Pathology and Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | - Seth J Corey
- Department of Cancer Biology, Cleveland Clinic, Cleveland, Ohio, USA
- Department of Pediatrics, Cleveland Clinic, Cleveland, Ohio, USA
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4
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Dobrewa W, Bielska M, Bąbol-Pokora K, Janczar S, Młynarski W. Congenital neutropenia: From lab bench to clinic bedside and back. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2024; 793:108476. [PMID: 37989463 DOI: 10.1016/j.mrrev.2023.108476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 11/11/2023] [Accepted: 11/12/2023] [Indexed: 11/23/2023]
Abstract
Neutropenia is a hematological condition characterized by a decrease in absolute neutrophil count (ANC) in peripheral blood, typically classified in adults as mild (1-1.5 × 109/L), moderate (0.5-1 × 109/L), or severe (< 0.5 × 109/L). It can be categorized into two types: congenital and acquired. Congenital severe chronic neutropenia (SCN) arises from mutations in various genes, with different inheritance patterns, including autosomal recessive, autosomal dominant, and X-linked forms, often linked to mitochondrial diseases. The most common genetic cause is alterations in the ELANE gene. Some cases exist as non-syndromic neutropenia within the SCN spectrum, where genetic origins remain unidentified. The clinical consequences of congenital neutropenia depend on granulocyte levels and dysfunction. Infants with this condition often experience recurrent bacterial infections, with approximately half facing severe infections within their first six months of life. These infections commonly affect the respiratory system, digestive tract, and skin, resulting in symptoms like fever, abscesses, and even sepsis. The severity of these symptoms varies, and the specific organs and systems affected depend on the genetic defect. Congenital neutropenia elevates the risk of developing acute myeloid leukemia (AML) or myelodysplastic syndromes (MDS), particularly with certain genetic variants. SCN patients may acquire CSF3R and RUNX1 mutations, which can predict the development of leukemia. It is important to note that high-dose granulocyte colony-stimulating factor (G-CSF) treatment may have the potential to promote leukemogenesis. Treatment for neutropenia involves antibiotics, drugs that boost neutrophil production, or bone marrow transplants. Immediate treatment is essential due to the heightened risk of severe infections. In severe congenital or cyclic neutropenia (CyN), the primary therapy is G-CSF, often combined with antibiotics. The G-CSF dosage is gradually increased to normalize neutrophil counts. Hematopoietic stem cell transplants are considered for non-responders or those at risk of AML/MDS. In cases of WHIM syndrome, CXCR4 inhibitors can be effective. Future treatments may involve gene editing and the use of the diabetes drug empagliflozin to alleviate neutropenia symptoms.
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Affiliation(s)
- Weronika Dobrewa
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, 36\50 Sporna Str, 91-738 Lodz, Poland.
| | - Marta Bielska
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, 36\50 Sporna Str, 91-738 Lodz, Poland
| | - Katarzyna Bąbol-Pokora
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, 36\50 Sporna Str, 91-738 Lodz, Poland
| | - Szymon Janczar
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, 36\50 Sporna Str, 91-738 Lodz, Poland
| | - Wojciech Młynarski
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, 36\50 Sporna Str, 91-738 Lodz, Poland.
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5
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Johansson KB, Zimmerman MS, Dmytrenko IV, Gao F, Link DC. Idasanutlin and navitoclax induce synergistic apoptotic cell death in T-cell acute lymphoblastic leukemia. Leukemia 2023; 37:2356-2366. [PMID: 37838759 PMCID: PMC10681904 DOI: 10.1038/s41375-023-02057-x] [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: 01/18/2023] [Revised: 09/24/2023] [Accepted: 10/04/2023] [Indexed: 10/16/2023]
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematologic malignancy in which activating mutations in the Notch pathway are thought to contribute to transformation, in part, by activating c-Myc. Increased c-Myc expression induces oncogenic stress that can trigger apoptosis through the MDM2-p53 tumor suppressor pathway. Since the great majority of T-ALL cases carry inactivating mutations upstream in this pathway but maintain wildtype MDM2 and TP53, we hypothesized that T-ALL would be selectively sensitive to MDM2 inhibition. Treatment with idasanutlin, an MDM2 inhibitor, induced only modest apoptosis in T-ALL cells but upregulated the pro-apoptotic BH3 domain genes BAX and BBC3, prompting us to evaluate the combination of idasanutlin with BH3 mimetics. Combination treatment with idasanutlin and navitoclax, a potent Bcl-2/Bcl-xL inhibitor, induces more consistent and potent synergistic killing of T-ALL PDX lines in vitro than venetoclax, a Bcl-2 specific inhibitor. Moreover, a marked synergic response to combination treatment with idasanutlin and navitoclax was seen in vivo in all four T-ALL xenografts tested, with a significant increase in overall survival in the combination treatment group. Collectively, these preclinical data show that the combination of idasanutlin and navitoclax is highly active in T-ALL and may merit consideration in the clinical setting.
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Affiliation(s)
- Kimberly B Johansson
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Medical Scientist Training Program, Washington University School of Medicine, St. Louis, MO, USA
| | - Megan S Zimmerman
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Iryna V Dmytrenko
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Feng Gao
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Daniel C Link
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
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6
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Lee S, Lee SB, Sung N, Xu WW, Chang C, Kim HE, Catic A, Tsai FTF. Structural basis of impaired disaggregase function in the oxidation-sensitive SKD3 mutant causing 3-methylglutaconic aciduria. Nat Commun 2023; 14:2028. [PMID: 37041140 PMCID: PMC10090083 DOI: 10.1038/s41467-023-37657-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 03/23/2023] [Indexed: 04/13/2023] Open
Abstract
Mitochondria are critical to cellular and organismal health. To prevent damage, mitochondria have evolved protein quality control machines to survey and maintain the mitochondrial proteome. SKD3, also known as CLPB, is a ring-forming, ATP-fueled protein disaggregase essential for preserving mitochondrial integrity and structure. SKD3 deficiency causes 3-methylglutaconic aciduria type VII (MGCA7) and early death in infants, while mutations in the ATPase domain impair protein disaggregation with the observed loss-of-function correlating with disease severity. How mutations in the non-catalytic N-domain cause disease is unknown. Here, we show that the disease-associated N-domain mutation, Y272C, forms an intramolecular disulfide bond with Cys267 and severely impairs SKD3Y272C function under oxidizing conditions and in living cells. While Cys267 and Tyr272 are found in all SKD3 isoforms, isoform-1 features an additional α-helix that may compete with substrate-binding as suggested by crystal structure analyses and in silico modeling, underscoring the importance of the N-domain to SKD3 function.
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Affiliation(s)
- Sukyeong Lee
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Advanced Technology Core for Macromolecular X-ray Crystallography, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sang Bum Lee
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Advanced Technology Core for Macromolecular X-ray Crystallography, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Nuri Sung
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Wendy W Xu
- Advanced Technology Core for Macromolecular X-ray Crystallography, Baylor College of Medicine, Houston, TX, 77030, USA
- Louisiana State University Health New Orleans School of Medicine, New Orleans, LA, 70112, USA
| | - Changsoo Chang
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Hyun-Eui Kim
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Andre Catic
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | - Francis T F Tsai
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.
- Advanced Technology Core for Macromolecular X-ray Crystallography, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA.
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7
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Wu D, Liu Y, Dai Y, Wang G, Lu G, Chen Y, Li N, Lin J, Gao N. Comprehensive structural characterization of the human AAA+ disaggregase CLPB in the apo- and substrate-bound states reveals a unique mode of action driven by oligomerization. PLoS Biol 2023; 21:e3001987. [PMID: 36745679 PMCID: PMC9934407 DOI: 10.1371/journal.pbio.3001987] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 02/16/2023] [Accepted: 01/04/2023] [Indexed: 02/07/2023] Open
Abstract
The human AAA+ ATPase CLPB (SKD3) is a protein disaggregase in the mitochondrial intermembrane space (IMS) and functions to promote the solubilization of various mitochondrial proteins. Loss-of-function CLPB mutations are associated with a few human diseases with neutropenia and neurological disorders. Unlike canonical AAA+ proteins, CLPB contains a unique ankyrin repeat domain (ANK) at its N-terminus. How CLPB functions as a disaggregase and the role of its ANK domain are currently unclear. Herein, we report a comprehensive structural characterization of human CLPB in both the apo- and substrate-bound states. CLPB assembles into homo-tetradecamers in apo-state and is remodeled into homo-dodecamers upon substrate binding. Conserved pore-loops (PLs) on the ATPase domains form a spiral staircase to grip and translocate the substrate in a step-size of 2 amino acid residues. The ANK domain is not only responsible for maintaining the higher-order assembly but also essential for the disaggregase activity. Interactome analysis suggests that the ANK domain may directly interact with a variety of mitochondrial substrates. These results reveal unique properties of CLPB as a general disaggregase in mitochondria and highlight its potential as a target for the treatment of various mitochondria-related diseases.
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Affiliation(s)
- Damu Wu
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Yan Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yuhao Dai
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
- Academy of Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Guopeng Wang
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Guoliang Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yan Chen
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Ningning Li
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
- Changping Laboratory, Beijing, China
| | - Jinzhong Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
- * E-mail: (JL); (NG)
| | - Ning Gao
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
- Changping Laboratory, Beijing, China
- National Biomedical Imaging Center, Peking University, Beijing, China
- * E-mail: (JL); (NG)
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Lee G, Kim RS, Lee SB, Lee S, Tsai FT. Deciphering the mechanism and function of Hsp100 unfoldases from protein structure. Biochem Soc Trans 2022; 50:1725-1736. [PMID: 36454589 PMCID: PMC9784670 DOI: 10.1042/bst20220590] [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: 10/10/2022] [Revised: 11/11/2022] [Accepted: 11/15/2022] [Indexed: 12/02/2022]
Abstract
Hsp100 chaperones, also known as Clp proteins, constitute a family of ring-forming ATPases that differ in 3D structure and cellular function from other stress-inducible molecular chaperones. While the vast majority of ATP-dependent molecular chaperones promote the folding of either the nascent chain or a newly imported polypeptide to reach its native conformation, Hsp100 chaperones harness metabolic energy to perform the reverse and facilitate the unfolding of a misfolded polypeptide or protein aggregate. It is now known that inside cells and organelles, different Hsp100 members are involved in rescuing stress-damaged proteins from a previously aggregated state or in recycling polypeptides marked for degradation. Protein degradation is mediated by a barrel-shaped peptidase that physically associates with the Hsp100 hexamer to form a two-component system. Notable examples include the ClpA:ClpP (ClpAP) and ClpX:ClpP (ClpXP) proteases that resemble the ring-forming FtsH and Lon proteases, which unlike ClpAP and ClpXP, feature the ATP-binding and proteolytic domains in a single polypeptide chain. Recent advances in electron cryomicroscopy (cryoEM) together with single-molecule biophysical studies have now provided new mechanistic insight into the structure and function of this remarkable group of macromolecular machines.
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Affiliation(s)
- Grace Lee
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Rice University, Houston, Texas 77005, USA
| | - Rebecca S. Kim
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Sang Bum Lee
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Sukyeong Lee
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Advanced Technology Core for Macromolecular X-ray Crystallography, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Francis T.F. Tsai
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Advanced Technology Core for Macromolecular X-ray Crystallography, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA
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Baker MJ, Crameri JJ, Thorburn DR, Frazier AE, Stojanovski D. Mitochondrial biology and dysfunction in secondary mitochondrial disease. Open Biol 2022; 12:220274. [PMID: 36475414 PMCID: PMC9727669 DOI: 10.1098/rsob.220274] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Mitochondrial diseases are a broad, genetically heterogeneous class of metabolic disorders characterized by deficits in oxidative phosphorylation (OXPHOS). Primary mitochondrial disease (PMD) defines pathologies resulting from mutation of mitochondrial DNA (mtDNA) or nuclear genes affecting either mtDNA expression or the biogenesis and function of the respiratory chain. Secondary mitochondrial disease (SMD) arises due to mutation of nuclear-encoded genes independent of, or indirectly influencing OXPHOS assembly and operation. Despite instances of novel SMD increasing year-on-year, PMD is much more widely discussed in the literature. Indeed, since the implementation of next generation sequencing (NGS) techniques in 2010, many novel mitochondrial disease genes have been identified, approximately half of which are linked to SMD. This review will consolidate existing knowledge of SMDs and outline discrete categories within which to better understand the diversity of SMD phenotypes. By providing context to the biochemical and molecular pathways perturbed in SMD, we hope to further demonstrate the intricacies of SMD pathologies outside of their indirect contribution to mitochondrial energy generation.
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Affiliation(s)
- Megan J. Baker
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Jordan J. Crameri
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3052, Australia
| | - David R. Thorburn
- Murdoch Children's Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Parkville, Victoria 3052, Australia,Victorian Clinical Genetics Services, Royal Children's Hospital, Parkville, Victoria 3052, Australia
| | - Ann E. Frazier
- Murdoch Children's Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Diana Stojanovski
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3052, Australia
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Tucker EJ, Baker MJ, Hock DH, Warren JT, Jaillard S, Bell KM, Sreenivasan R, Bakhshalizadeh S, Hanna CA, Caruana NJ, Wortmann SB, Rahman S, Pitceathly RDS, Donadieu J, Alimi A, Launay V, Coppo P, Christin-Maitre S, Robevska G, van den Bergen J, Kline BL, Ayers KL, Stewart PN, Stroud DA, Stojanovski D, Sinclair AH. Premature Ovarian Insufficiency in CLPB Deficiency: Transcriptomic, Proteomic and Phenotypic Insights. J Clin Endocrinol Metab 2022; 107:3328-3340. [PMID: 36074910 PMCID: PMC9693831 DOI: 10.1210/clinem/dgac528] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Indexed: 11/19/2022]
Abstract
CONTEXT Premature ovarian insufficiency (POI) is a common form of female infertility that usually presents as an isolated condition but can be part of various genetic syndromes. Early diagnosis and treatment of POI can minimize comorbidity and improve health outcomes. OBJECTIVE We aimed to determine the genetic cause of syndromic POI, intellectual disability, neutropenia, and cataracts. METHODS We performed whole-exome sequencing (WES) followed by functional validation via RT-PCR, RNAseq, and quantitative proteomics, as well as clinical update of previously reported patients with variants in the caseinolytic peptidase B (CLPB) gene. RESULTS We identified causative variants in CLPB, encoding a mitochondrial disaggregase. Variants in this gene are known to cause an autosomal recessive syndrome involving 3-methylglutaconic aciduria, neurological dysfunction, cataracts, and neutropenia that is often fatal in childhood; however, there is likely a reporting bias toward severe cases. Using RNAseq and quantitative proteomics we validated causation and gained insight into genotype:phenotype correlation. Clinical follow-up of patients with CLPB deficiency who survived to adulthood identified POI and infertility as a common postpubertal ailment. CONCLUSION A novel splicing variant is associated with CLPB deficiency in an individual who survived to adulthood. POI is a common feature of postpubertal female individuals with CLPB deficiency. Patients with CLPB deficiency should be referred to pediatric gynecologists/endocrinologists for prompt POI diagnosis and hormone replacement therapy to minimize associated comorbidities.
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Affiliation(s)
- Elena J Tucker
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Megan J Baker
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Daniella H Hock
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Julia T Warren
- Division of Hematology-Oncology, Department of Pediatrics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Sylvie Jaillard
- Univ Rennes, CHU Rennes, INSERM, EHESP, IRSET (Institut de recherche en santé, environnement et travail)—UMR_S 1085, F-35000 Rennes, France
- CHU Rennes, Service de Cytogénétique et Biologie Cellulaire, F-35033 Rennes, France
| | - Katrina M Bell
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Rajini Sreenivasan
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Shabnam Bakhshalizadeh
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Chloe A Hanna
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia
- Department of Gynaecology, The Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Nikeisha J Caruana
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
- Institute for Health and Sport (IHES), Victoria University, Melbourne, VIC, 3011, Australia
| | - Saskia B Wortmann
- University Children's Hospital, Paracelsus Medical University (PMU), Salzburg 5020, Austria
- Radboud Center for Mitochondrial Medicine, Department of Pediatrics, Amalia Children's Hospital, Radboudumc, Nijmegen 6524, The Netherlands
| | - Shamima Rahman
- Mitochondrial Research Group, UCL Great Ormond Street Institute of Child Health, and Metabolic Unit, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Robert D S Pitceathly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, WC1N 3BG, UK
| | - Jean Donadieu
- Sorbonne Université, Service d’Hémato-oncologie Pédiatrique, Assistance Publique-Hopitaux de Paris (AP-HP), Hôpital Trousseau, Paris 75006, France
- Registre Français des Neutropénies Congénitales, Hôpital Trousseau, Paris 75006, France
- Centre de Référence des Neutropénies Chroniques, AP-HP, Hôpital Trousseau, Paris 75006, France
| | - Aurelia Alimi
- Sorbonne Université, Service d’Hémato-oncologie Pédiatrique, Assistance Publique-Hopitaux de Paris (AP-HP), Hôpital Trousseau, Paris 75006, France
- Registre Français des Neutropénies Congénitales, Hôpital Trousseau, Paris 75006, France
- Centre de Référence des Neutropénies Chroniques, AP-HP, Hôpital Trousseau, Paris 75006, France
| | - Vincent Launay
- Hematologie, Centre Hospitalier de St Brieuc, Paris 22027, France
| | - Paul Coppo
- Sorbonne Université, Service d’hématologie Hôpital Saint-Antoine, AP-HP, Paris75006, France
| | - Sophie Christin-Maitre
- Sorbonne Université, Service d’Endocrinologie, diabétologie et médecine de la reproduction Hôpital Saint-Antoine, AP-HP, Paris75006, France
| | - Gorjana Robevska
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Jocelyn van den Bergen
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Brianna L Kline
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Katie L Ayers
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Phoebe N Stewart
- Department of Paediatrics, The Royal Hobart Hospital, Tasmania 7000, Australia
| | - David A Stroud
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Diana Stojanovski
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Andrew H Sinclair
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia
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11
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Cupo RR, Rizo AN, Braun GA, Tse E, Chuang E, Gupta K, Southworth DR, Shorter J. Unique structural features govern the activity of a human mitochondrial AAA+ disaggregase, Skd3. Cell Rep 2022; 40:111408. [PMID: 36170828 PMCID: PMC9584538 DOI: 10.1016/j.celrep.2022.111408] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 06/02/2022] [Accepted: 09/01/2022] [Indexed: 11/27/2022] Open
Abstract
The AAA+ protein, Skd3 (human CLPB), solubilizes proteins in the mitochondrial intermembrane space, which is critical for human health. Skd3 variants with defective protein-disaggregase activity cause severe congenital neutropenia (SCN) and 3-methylglutaconic aciduria type 7 (MGCA7). How Skd3 disaggregates proteins remains poorly understood. Here, we report a high-resolution structure of a Skd3-substrate complex. Skd3 adopts a spiral hexameric arrangement that engages substrate via pore-loop interactions in the nucleotide-binding domain (NBD). Substrate-bound Skd3 hexamers stack head-to-head via unique, adaptable ankyrin-repeat domain (ANK)-mediated interactions to form dodecamers. Deleting the ANK linker region reduces dodecamerization and disaggregase activity. We elucidate apomorphic features of the Skd3 NBD and C-terminal domain that regulate disaggregase activity. We also define how Skd3 subunits collaborate to disaggregate proteins. Importantly, SCN-linked subunits sharply inhibit disaggregase activity, whereas MGCA7-linked subunits do not. These advances illuminate Skd3 structure and mechanism, explain SCN and MGCA7 inheritance patterns, and suggest therapeutic strategies.
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Affiliation(s)
- Ryan R Cupo
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA; Pharmacology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alexandrea N Rizo
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA; Graduate Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA
| | - Gabriel A Braun
- Chemistry and Chemical Biology Graduate Program, Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Eric Tse
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Edward Chuang
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA; Pharmacology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kushol Gupta
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel R Southworth
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
| | - James Shorter
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA; Pharmacology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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12
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The Bacterial ClpXP-ClpB Family Is Enriched with RNA-Binding Protein Complexes. Cells 2022; 11:cells11152370. [PMID: 35954215 PMCID: PMC9368063 DOI: 10.3390/cells11152370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/23/2022] [Accepted: 07/28/2022] [Indexed: 11/17/2022] Open
Abstract
In the matrix of bacteria/mitochondria/chloroplasts, Lon acts as the degradation machine for soluble proteins. In stress periods, however, proteostasis and survival depend on the strongly conserved Clp/Hsp100 family. Currently, the targets of ATP-powered unfoldases/disaggregases ClpB and ClpX and of peptidase ClpP heptameric rings are still unclear. Trapping experiments and proteome profiling in multiple organisms triggered confusion, so we analyzed the consistency of ClpP-trap targets in bacteria. We also provide meta-analyses of protein interactions in humans, to elucidate where Clp family members are enriched. Furthermore, meta-analyses of mouse complexomics are provided. Genotype–phenotype correlations confirmed our concept. Trapping, proteome, and complexome data retrieved consistent coaccumulation of CLPXP with GFM1 and TUFM orthologs. CLPX shows broad interaction selectivity encompassing mitochondrial translation elongation, RNA granules, and nucleoids. CLPB preferentially attaches to mitochondrial RNA granules and translation initiation components; CLPP is enriched with them all and associates with release/recycling factors. Mutations in CLPP cause Perrault syndrome, with phenotypes similar to defects in mtDNA/mtRNA. Thus, we propose that CLPB and CLPXP are crucial to counteract misfolded insoluble protein assemblies that contain nucleotides. This insight is relevant to improve ClpP-modulating drugs that block bacterial growth and for the treatment of human infertility, deafness, and neurodegeneration.
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13
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Fan Y, Murgia M, Linder MI, Mizoguchi Y, Wang C, Łyszkiewicz M, Ziȩtara N, Liu Y, Frenz S, Sciuccati G, Partida-Gaytan A, Alizadeh Z, Rezaei N, Rehling P, Dennerlein S, Mann M, Klein C. HAX1-dependent control of mitochondrial proteostasis governs neutrophil granulocyte differentiation. J Clin Invest 2022; 132:153153. [PMID: 35499078 PMCID: PMC9057593 DOI: 10.1172/jci153153] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 03/10/2022] [Indexed: 01/18/2023] Open
Abstract
The relevance of molecular mechanisms governing mitochondrial proteostasis to the differentiation and function of hematopoietic and immune cells is largely elusive. Through dissection of the network of proteins related to HCLS1-associated protein X-1, we defined a potentially novel functional CLPB/HAX1/(PRKD2)/HSP27 axis with critical importance for the differentiation of neutrophil granulocytes and, thus, elucidated molecular and metabolic mechanisms underlying congenital neutropenia in patients with HAX1 deficiency as well as bi- and monoallelic mutations in CLPB. As shown by stable isotope labeling by amino acids in cell culture (SILAC) proteomics, CLPB and HAX1 control the balance of mitochondrial protein synthesis and persistence crucial for proper mitochondrial function. Impaired mitochondrial protein dynamics are associated with decreased abundance of the serine-threonine kinase PRKD2 and HSP27 phosphorylated on serines 78 and 82. Cellular defects in HAX1–/– cells can be functionally reconstituted by HSP27. Thus, mitochondrial proteostasis emerges as a critical molecular and metabolic mechanism governing the differentiation and function of neutrophil granulocytes.
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Affiliation(s)
- Yanxin Fan
- Department of Pediatrics, Dr. von Hauner Children’s Hospital and Gene Center, University Hospital, Ludwig-Maximilians-Universität (LMU), Munich, Germany
| | - Marta Murgia
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | - Monika I. Linder
- Department of Pediatrics, Dr. von Hauner Children’s Hospital and Gene Center, University Hospital, Ludwig-Maximilians-Universität (LMU), Munich, Germany
| | - Yoko Mizoguchi
- Department of Pediatrics, Dr. von Hauner Children’s Hospital and Gene Center, University Hospital, Ludwig-Maximilians-Universität (LMU), Munich, Germany
| | - Cong Wang
- Department of Cellular Biochemistry, University Medical Center Goettingen, Goettingen, Germany
| | - Marcin Łyszkiewicz
- Department of Pediatrics, Dr. von Hauner Children’s Hospital and Gene Center, University Hospital, Ludwig-Maximilians-Universität (LMU), Munich, Germany
| | - Natalia Ziȩtara
- Department of Pediatrics, Dr. von Hauner Children’s Hospital and Gene Center, University Hospital, Ludwig-Maximilians-Universität (LMU), Munich, Germany
| | - Yanshan Liu
- Department of Pediatrics, Dr. von Hauner Children’s Hospital and Gene Center, University Hospital, Ludwig-Maximilians-Universität (LMU), Munich, Germany
| | - Stephanie Frenz
- Department of Pediatrics, Dr. von Hauner Children’s Hospital and Gene Center, University Hospital, Ludwig-Maximilians-Universität (LMU), Munich, Germany
| | - Gabriela Sciuccati
- Hematology and Oncology Department, Hospital de Pediatria “Prof. Dr. J.P. Garrahan,” Buenos Aires, Argentina
| | - Armando Partida-Gaytan
- Unidad de Investigación en Inmunodeficiencias Primarias, Instituto Nacional de Pediatría, Mexico City, Mexico
| | | | - Nima Rezaei
- Research Center for Immunodeficiencies, Children’s Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Goettingen, Goettingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells,” University of Goettingen, Goettingen, Germany
- Max Planck Institute for Biophysical Chemistry, Goettingen, Germany
| | - Sven Dennerlein
- Department of Cellular Biochemistry, University Medical Center Goettingen, Goettingen, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Christoph Klein
- Department of Pediatrics, Dr. von Hauner Children’s Hospital and Gene Center, University Hospital, Ludwig-Maximilians-Universität (LMU), Munich, Germany
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14
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Rivalta B, Torraco A, Martinelli D, Luciani M, Carrozzo R, Finocchi A. Biallelic CLPB mutation associated with isolated neutropenia and 3-MGA-uria. Pediatr Allergy Immunol 2022; 33:e13782. [PMID: 35616898 PMCID: PMC9325556 DOI: 10.1111/pai.13782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Beatrice Rivalta
- Research Unit of Primary Immunodeficiencies, Immune and Infectious Diseases Division, Academic Department of Pediatrics (DPUO), Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.,Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Alessandra Torraco
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Department of Neurosciences, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Diego Martinelli
- Division of Metabolism, Bambino Gesù Children Hospital and Research Institute, IRCCS, Rome, Italy
| | - Matteo Luciani
- Department of Pediatric Hemato-Oncology and Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Rosalba Carrozzo
- Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Andrea Finocchi
- Research Unit of Primary Immunodeficiencies, Immune and Infectious Diseases Division, Academic Department of Pediatrics (DPUO), Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.,Chair of Pediatrics, Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
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15
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Ward LD, Parker MM, Deaton AM, Tu HC, Flynn-Carroll AO, Hinkle G, Nioi P. Rare coding variants in DNA damage repair genes associated with timing of natural menopause. HGG ADVANCES 2022; 3:100079. [PMID: 35493704 PMCID: PMC9039695 DOI: 10.1016/j.xhgg.2021.100079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 12/08/2021] [Indexed: 11/30/2022] Open
Abstract
The age of menopause is associated with fertility and disease risk, and its genetic control is of great interest. We use whole-exome sequences from 132,370 women in the UK Biobank to test for associations between rare damaging variants and age at natural menopause. Rare damaging variants in five genes are significantly associated with menopause: CHEK2 (p = 3.3 × 10−51), DCLRE1A (p = 8.4 × 10−13), and HELB (p = 5.7 × 10−7) with later menopause and TOP3A (p = 7.6 × 10−8) and CLPB (p = 8.1 × 10−7) with earlier menopause. Two additional genes are suggestive: RAD54L (p = 2.4 × 10−6) with later menopause and HROB (p = 2.9 × 10−6) with earlier menopause. In a follow-up analysis of repeated questionnaires in women who were initially premenopausal, CHEK2, TOP3A, and RAD54L genotypes are associated with subsequent menopause. Consistent with previous genome-wide association studies (GWASs), six of the seven genes are involved in the DNA damage repair pathway. Phenome-wide scans across 398,569 men and women revealed that in addition to known associations with cancers and blood cell counts, rare variants in CHEK2 are also associated with increased risk for uterine fibroids, polycystic ovary syndrome, and prostate hypertrophy; these associations are not shared with higher-penetrance breast cancer genes. Causal mediation analysis suggests that approximately 8% of the breast cancer risk conferred by CHEK2 pathogenic variants after menopause is mediated through delayed menopause.
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16
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AAA+ proteins: one motor, multiple ways to work. Biochem Soc Trans 2022; 50:895-906. [PMID: 35356966 DOI: 10.1042/bst20200350] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 12/15/2022]
Abstract
Numerous ATPases associated with diverse cellular activities (AAA+) proteins form hexameric, ring-shaped complexes that function via ATPase-coupled translocation of substrates across the central channel. Cryo-electron microscopy of AAA+ proteins processing substrate has revealed non-symmetric, staircase-like hexameric structures that indicate a sequential clockwise/2-residue step translocation model for these motors. However, for many of the AAA+ proteins that share similar structural features, their translocation properties have not yet been experimentally determined. In the cases where translocation mechanisms have been determined, a two-residue translocation step-size has not been resolved. In this review, we explore Hsp104, ClpB, ClpA and ClpX as examples to review the experimental methods that have been used to examine, in solution, the translocation mechanisms employed by AAA+ motor proteins. We then ask whether AAA+ motors sharing similar structural features can have different translocation mechanisms. Finally, we discuss whether a single AAA+ motor can adopt multiple translocation mechanisms that are responsive to different challenges imposed by the substrate or the environment. We suggest that AAA+ motors adopt more than one translocation mechanism and are tuned to switch to the most energetically efficient mechanism when constraints are applied.
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17
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Spaulding Z, Thevarajan I, Schrag LG, Zubcevic L, Zolkiewska A, Zolkiewski M. Human mitochondrial AAA+ ATPase SKD3/CLPB assembles into nucleotide-stabilized dodecamers. Biochem Biophys Res Commun 2022; 602:21-26. [PMID: 35247700 PMCID: PMC8957611 DOI: 10.1016/j.bbrc.2022.02.101] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 02/24/2022] [Indexed: 12/01/2022]
Abstract
SKD3, also known as human CLPB, belongs to the AAA+ family of ATPases associated with various activities. Mutations in the SKD3/CLPB gene cause 3-methylglutaconic aciduria type VII and congenital neutropenia. SKD3 is upregulated in acute myeloid leukemia, where it contributes to anti-cancer drug resistance. SKD3 resides in the mitochondrial intermembrane space, where it forms ATP-dependent high-molecular weight complexes, but its biological function and mechanistic links to the clinical phenotypes are currently unknown. Using sedimentation equilibrium and dynamic light scattering, we show that SKD3 is monomeric at low protein concentration in the absence of nucleotides, but it forms oligomers at higher protein concentration or in the presence of adenine nucleotides. The apparent molecular weight of the nucleotide-bound SKD3 is consistent with self-association of 12 monomers. Image-class analysis and averaging from negative-stain electron microscopy (EM) of SKD3 in the ATP-bound state visualized cylinder-shaped particles with an open central channel along the cylinder axis. The dimensions of the EM-visualized particle suggest that the SKD3 dodecamer is formed by association of two hexameric rings. While hexameric structure has been often observed among AAA+ ATPases, a double-hexamer sandwich found for SKD3 appears uncommon within this protein family. A functional significance of the non-canonical structure of SKD3 remains to be determined.
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Affiliation(s)
- Zachary Spaulding
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA
| | - Indhujah Thevarajan
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA
| | - Lynn G Schrag
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Lejla Zubcevic
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Anna Zolkiewska
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA
| | - Michal Zolkiewski
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA.
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18
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CLPB in neutropenia: 1 gene with many faces. Blood 2022; 139:649-650. [PMID: 35113147 DOI: 10.1182/blood.2021012606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 11/20/2022] Open
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19
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Wu Z, Gong H, Zhou Z, Jiang T, Lin Z, Li J, Xiao S, Yang B, Huang L. Mapping short tandem repeats for liver gene expression traits helps prioritize potential causal variants for complex traits in pigs. J Anim Sci Biotechnol 2022; 13:8. [PMID: 35034641 PMCID: PMC8762894 DOI: 10.1186/s40104-021-00658-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 11/25/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Short tandem repeats (STRs) were recently found to have significant impacts on gene expression and diseases in humans, but their roles on gene expression and complex traits in pigs remain unexplored. This study investigates the effects of STRs on gene expression in liver tissues based on the whole-genome sequences and RNA-Seq data of a discovery cohort of 260 F6 individuals and a validation population of 296 F7 individuals from a heterogeneous population generated from crosses among eight pig breeds. RESULTS We identified 5203 and 5868 significantly expression STRs (eSTRs, FDR < 1%) in the F6 and F7 populations, respectively, most of which could be reciprocally validated (π1 = 0.92). The eSTRs explained 27.5% of the cis-heritability of gene expression traits on average. We further identified 235 and 298 fine-mapped STRs through the Bayesian fine-mapping approach in the F6 and F7 pigs, respectively, which were significantly enriched in intron, ATAC peak, compartment A and H3K4me3 regions. We identified 20 fine-mapped STRs located in 100 kb windows upstream and downstream of published complex trait-associated SNPs, which colocalized with epigenetic markers such as H3K27ac and ATAC peaks. These included eSTR of the CLPB, PGLS, PSMD6 and DHDH genes, which are linked with genome-wide association study (GWAS) SNPs for blood-related traits, leg conformation, growth-related traits, and meat quality traits, respectively. CONCLUSIONS This study provides insights into the effects of STRs on gene expression traits. The identified eSTRs are valuable resources for prioritizing causal STRs for complex traits in pigs.
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Affiliation(s)
- Zhongzi Wu
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Huanfa Gong
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Zhimin Zhou
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Tao Jiang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Ziqi Lin
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Jing Li
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Shijun Xiao
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Bin Yang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China.
| | - Lusheng Huang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China.
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20
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Touw IP. Congenital neutropenia: disease models guiding new treatment strategies. Curr Opin Hematol 2022; 29:27-33. [PMID: 34854832 PMCID: PMC8654271 DOI: 10.1097/moh.0000000000000696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
PURPOSE OF REVIEW Myeloid diseases are often characterized by a disturbed regulation of myeloid cell proliferation, survival, and maturation. This may either result in a severe paucity of functional neutrophils (neutropenia), an excess production of mature cells (myeloproliferative disorders) or in clonal expansions of dysplastic or immature myeloid cells (myelodysplasia and acute myeloid leukemia). Although these conditions can be regarded as separate entities, caused by the accumulation of distinct sets of somatic gene mutations, it becomes increasingly clear that they may also evolve as the prime consequence of a congenital defect resulting in severe neutropenia. Prominent examples of such conditions include the genetically heterogeneous forms of severe congenital neutropenia (SCN) and Shwachman-Diamond Syndrome. CSF3 treatment is a successful therapy to alleviate neutropenia in the majority of these patients but does not cure the disease nor does it prevent malignant transformation. Allogeneic stem cell transplantation is currently the only therapeutic option to cure SCN, but is relatively cumbersome, e.g., hampered by treatment-related mortality and donor availability. Hence, there is a need for new therapeutic approaches. RECENT FINDINGS Developments in disease modeling, amongst others based on induced pluripotent stem cell and CRISPR/Cas9 based gene-editing technologies, have created new insights in disease biology and possibilities for treatment. In addition, they are fueling expectations for advanced disease monitoring to prevent malignant transformation. SUMMARY This review highlights the recent progress made in SCN disease modeling and discusses the challenges that are still ahead of us to gain a better understanding of the biological heterogeneity of the disease and its consequences for patient care.
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Affiliation(s)
- Ivo P Touw
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
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