1
|
Rips J, Halstuk O, Fuchs A, Lang Z, Sido T, Gershon-Naamat S, Abu-Libdeh B, Edvardson S, Salah S, Breuer O, Hadhud M, Eden S, Simon I, Slae M, Damseh NS, Abu-Libdeh A, Eskin-Schwartz M, Birk OS, Varga J, Schueler-Furman O, Rosenbluh C, Elpeleg O, Yanovsky-Dagan S, Mor-Shaked H, Harel T. Unbiased phenotype and genotype matching maximizes gene discovery and diagnostic yield. Genet Med 2024; 26:101068. [PMID: 38193396 DOI: 10.1016/j.gim.2024.101068] [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: 08/11/2023] [Revised: 12/31/2023] [Accepted: 01/04/2024] [Indexed: 01/10/2024] Open
Abstract
PURPOSE Widespread application of next-generation sequencing, combined with data exchange platforms, has provided molecular diagnoses for countless families. To maximize diagnostic yield, we implemented an unbiased semi-automated genematching algorithm based on genotype and phenotype matching. METHODS Rare homozygous variants identified in 2 or more affected individuals, but not in healthy individuals, were extracted from our local database of ∼12,000 exomes. Phenotype similarity scores (PSS), based on human phenotype ontology terms, were assigned to each pair of individuals matched at the genotype level using HPOsim. RESULTS 33,792 genotype-matched pairs were discovered, representing variants in 7567 unique genes. There was an enrichment of PSS ≥0.1 among pathogenic/likely pathogenic variant-level pairs (94.3% in pathogenic/likely pathogenic variant-level matches vs 34.75% in all matches). We highlighted founder or region-specific variants as an internal positive control and proceeded to identify candidate disease genes. Variant-level matches were particularly helpful in cases involving inframe indels and splice region variants beyond the canonical splice sites, which may otherwise have been disregarded, allowing for detection of candidate disease genes, such as KAT2A, RPAIN, and LAMP3. CONCLUSION Semi-automated genotype matching combined with PSS is a powerful tool to resolve variants of uncertain significance and to identify candidate disease genes.
Collapse
Affiliation(s)
- Jonathan Rips
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel
| | - Orli Halstuk
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel; Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Adina Fuchs
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel; Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Ziv Lang
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel
| | - Tal Sido
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel
| | | | - Bassam Abu-Libdeh
- Department of Pediatrics & Genetics, Makassed Hospital & Al-Quds Medical School, E. Jerusalem, Palestine
| | - Simon Edvardson
- Faculty of Medicine, Hebrew University of Jerusalem, Israel; Pediatric Neurology Unit, Hadassah Medical Center, Jerusalem, Israel
| | - Somaya Salah
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel
| | - Oded Breuer
- Faculty of Medicine, Hebrew University of Jerusalem, Israel; Pediatric Pulmonology and CF Unit, Department of Pediatrics, Hadassah Medical Center, Jerusalem, Israel
| | - Mohamad Hadhud
- Faculty of Medicine, Hebrew University of Jerusalem, Israel; Pediatric Pulmonology and CF Unit, Department of Pediatrics, Hadassah Medical Center, Jerusalem, Israel
| | - Sharon Eden
- Institute of Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Itamar Simon
- Institute of Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Mordechai Slae
- Pediatric Gastroenterology Unit, Department of Pediatrics, Hadassah Medical Center, Jerusalem, Israel
| | - Nadirah S Damseh
- Department of Pediatrics & Genetics, Makassed Hospital & Al-Quds Medical School, E. Jerusalem, Palestine
| | - Abdulsalam Abu-Libdeh
- Department of Pediatrics & Genetics, Makassed Hospital & Al-Quds Medical School, E. Jerusalem, Palestine; Division of Pediatric Endocrinology, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Marina Eskin-Schwartz
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel; Genetics Institute, Soroka University Medical Center, Beer-Sheva, Israel
| | - Ohad S Birk
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel; Genetics Institute, Soroka University Medical Center, Beer-Sheva, Israel
| | - Julia Varga
- Microbiology and Molecular Genetics, Institute for Biomedical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ora Schueler-Furman
- Microbiology and Molecular Genetics, Institute for Biomedical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Orly Elpeleg
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel; Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | | | - Hagar Mor-Shaked
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel; Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Tamar Harel
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel; Faculty of Medicine, Hebrew University of Jerusalem, Israel.
| |
Collapse
|
2
|
Choudhary D, Kaur A, Singh P, Chaudhary G, Kaur R, Bayan MF, Chandrasekaran B, Marji SM, Ayman R. Target protein degradation by protacs: A budding cancer treatment strategy. Pharmacol Ther 2023; 250:108525. [PMID: 37696366 DOI: 10.1016/j.pharmthera.2023.108525] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/25/2023] [Accepted: 08/30/2023] [Indexed: 09/13/2023]
Abstract
Cancer is one of the most common causes of death. So, its lethal effect increases with time. Near about hundreds of cancers are known in humans. Cancer treatment is done to cure or prolonged remission, and shrinkage of the tumor. Cytotoxic agents, biological agents/targeted drugs, hormonal drugs, surgery, radiotherapy/proton therapy, chemotherapy, immunotherapy, and gene therapy are currently used in the treatment of cancer but their cost is high and cause various side effects. Seeing this, some new targeted strategies such as PROTACs are the need of the time. Proteolysis targeting chimera (PROTAC) has become one of the most discussed topics regarding cancer treatment. Few of the PROTAC molecules are in the trial phases. PROTACs have many advantages over other strategies such as modularity, compatibility, sub-stoichiometric activity, acting on undruggable targets, molecular design, and acts on intracellular targets, selectivity and specificity can be recruited for any cancer, versatility, and others. PROTACs are having some unclear questions on their pharmacokinetics, heavy-molecular weight, etc. PROTACs are anticipated to bring about a conversion in current healthcare and will emerge as booming treatments. In this review article we summarize PROTACs, their mechanism of action, uses, advantages, disadvantages, challenges, and future aspects for the successful development of potent PROTACs as a drug strategy.
Collapse
Affiliation(s)
- Diksha Choudhary
- Chitkara College of Pharmacy, Chitkara University, Punjab 140401, India
| | - Amritpal Kaur
- Chitkara College of Pharmacy, Chitkara University, Punjab 140401, India
| | - Pargat Singh
- Chitkara College of Pharmacy, Chitkara University, Punjab 140401, India
| | - Gaurav Chaudhary
- Chitkara College of Pharmacy, Chitkara University, Punjab 140401, India
| | - Rajwinder Kaur
- Chitkara College of Pharmacy, Chitkara University, Punjab 140401, India.
| | - Mohammad F Bayan
- Faculty of Pharmacy, Philadelphia University, P.O. Box 1, Amman 19392, Jordan
| | | | - Saeed M Marji
- Faculty of Pharmacy, Philadelphia University, P.O. Box 1, Amman 19392, Jordan
| | - Reema Ayman
- Faculty of Pharmacy, Philadelphia University, P.O. Box 1, Amman 19392, Jordan
| |
Collapse
|
3
|
Calciolari B, Scarpinello G, Tubi LQ, Piazza F, Carrer A. Metabolic control of epigenetic rearrangements in B cell pathophysiology. Open Biol 2022; 12:220038. [PMID: 35580618 PMCID: PMC9113833 DOI: 10.1098/rsob.220038] [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] [Indexed: 01/04/2023] Open
Abstract
Both epigenetic and metabolic reprogramming guide lymphocyte differentiation and can be linked, in that metabolic inputs can be integrated into the epigenome to inform cell fate decisions. This framework has been thoroughly investigated in several pathophysiological contexts, including haematopoietic cell differentiation. In fact, metabolite availability dictates chromatin architecture and lymphocyte specification, a multi-step process where haematopoietic stem cells become terminally differentiated lymphocytes (effector or memory) to mount the adaptive immune response. B and T cell precursors reprogram their cellular metabolism across developmental stages, not only to meet ever-changing energetic demands but to impose chromatin accessibility and regulate the function of master transcription factors. Metabolic control of the epigenome has been extensively investigated in T lymphocytes, but how this impacts type-B life cycle remains poorly appreciated. This assay will review our current understanding of the connection between cell metabolism and epigenetics at crucial steps of B cell maturation and how its dysregulation contributes to malignant transformation.
Collapse
Affiliation(s)
- Beatrice Calciolari
- Department of Biology (DiBio), of the University of Padova, Padova, Italy,Department of Medicine (DIMED), Hematology and Clinical Immunology Section, of the University of Padova, Padova, Italy,Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Greta Scarpinello
- Department of Surgical, Oncological and Gastroenterological Sciences (DiSCOG), of the University of Padova, Padova, Italy
| | - Laura Quotti Tubi
- Department of Medicine (DIMED), Hematology and Clinical Immunology Section, of the University of Padova, Padova, Italy,Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Francesco Piazza
- Department of Medicine (DIMED), Hematology and Clinical Immunology Section, of the University of Padova, Padova, Italy,Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Alessandro Carrer
- Department of Biology (DiBio), of the University of Padova, Padova, Italy,Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
| |
Collapse
|