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Liu Y, Cheng H, Cheng M, Sun M, Ma J, Gong T. Next generation sequencing reveals the mutation landscape of Chinese MDS patients and the association between mutations and AML transformations. Hematology 2024; 29:2392469. [PMID: 39158486 DOI: 10.1080/16078454.2024.2392469] [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: 10/26/2023] [Accepted: 08/10/2024] [Indexed: 08/20/2024] Open
Abstract
BACKGROUND/OBJECTIVE Approximately 30% of patients with MDS eventually develop to acute myeloid leukemia (AML). Our study aimed to investigate the mutation landscape of Chinese MDS patients and identify the mutated genes which are closely implicated in the transformation of MDS to AML. METHODS In total, 412 sequencing data collected from 313 patients were used for analysis. Mutation frequencies between different groups were compared by Fisher's exact. A predictive model for risk of transformation/death of newly diagnosed patients was constructed by logistic regression. RESULTS The most frequently mutated genes in newly diagnosed patients were TP53, TET2, RUNX1, PIGA, and BCOR and mutations of RUNX1, TP53, BCORL1, TET2, and BCOR genes were more common in the treated MDS patients. Besides, we found that the mutation frequencies of IDH2, TET2, and EZH2 were significantly higher in MDS patients aged over 60 years. Moreover, two mutation sites, KRASG12A and TP53H140N were detected only at transformation in one patient, while not detected at diagnosis. In addition, the mutation frequencies of EZH2 V704F and TET2 I1873N were stable from diagnosis to transformation in two patients. Finally, we constructed a predictive model for risk of transformation/death of newly diagnosed patients combing detected data of 10 genes and the number of to leukocyte, with a sensitivity of 63.3% and a specificity of 84.6% in distinguishing individuals with and without risk of transformation/death. CONCLUSION In summary, our study found several mutations associated with the transformation from MDS to AML, and constructed a predictive model for risk of transformation/death of MDS patients.
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Affiliation(s)
- Yu Liu
- Institute of Harbin Hematology and Oncology, the first hospital of Harbin, Harbin, People's Republic of China
| | - Huanchen Cheng
- Institute of Harbin Hematology and Oncology, the first hospital of Harbin, Harbin, People's Republic of China
| | - Mei Cheng
- Institute of Harbin Hematology and Oncology, the first hospital of Harbin, Harbin, People's Republic of China
| | - Meng Sun
- Institute of Harbin Hematology and Oncology, the first hospital of Harbin, Harbin, People's Republic of China
| | - Jun Ma
- Institute of Harbin Hematology and Oncology, the first hospital of Harbin, Harbin, People's Republic of China
| | - Tiejun Gong
- Institute of Harbin Hematology and Oncology, the first hospital of Harbin, Harbin, People's Republic of China
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Jin X, Zhang R, Fu Y, Zhu Q, Hong L, Wu A, Wang H. Unveiling aging dynamics in the hematopoietic system insights from single-cell technologies. Brief Funct Genomics 2024; 23:639-650. [PMID: 38688725 DOI: 10.1093/bfgp/elae019] [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: 02/10/2024] [Revised: 04/10/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024] Open
Abstract
As the demographic structure shifts towards an aging society, strategies aimed at slowing down or reversing the aging process become increasingly essential. Aging is a major predisposing factor for many chronic diseases in humans. The hematopoietic system, comprising blood cells and their associated bone marrow microenvironment, intricately participates in hematopoiesis, coagulation, immune regulation and other physiological phenomena. The aging process triggers various alterations within the hematopoietic system, serving as a spectrum of risk factors for hematopoietic disorders, including clonal hematopoiesis, immune senescence, myeloproliferative neoplasms and leukemia. The emerging single-cell technologies provide novel insights into age-related changes in the hematopoietic system. In this review, we summarize recent studies dissecting hematopoietic system aging using single-cell technologies. We discuss cellular changes occurring during aging in the hematopoietic system at the levels of the genomics, transcriptomics, epigenomics, proteomics, metabolomics and spatial multi-omics. Finally, we contemplate the future prospects of single-cell technologies, emphasizing the impact they may bring to the field of hematopoietic system aging research.
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Affiliation(s)
- Xinrong Jin
- Zhejiang Key Laboratory of Medical Epigenetics, School of Basic Medical Sciences, The Third People's Hospital of Deqing, Deqing Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Ruohan Zhang
- Zhejiang Key Laboratory of Medical Epigenetics, School of Basic Medical Sciences, The Third People's Hospital of Deqing, Deqing Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Yunqi Fu
- Zhejiang Key Laboratory of Medical Epigenetics, School of Basic Medical Sciences, The Third People's Hospital of Deqing, Deqing Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Qiunan Zhu
- Zhejiang Key Laboratory of Medical Epigenetics, School of Basic Medical Sciences, The Third People's Hospital of Deqing, Deqing Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Liquan Hong
- Zhejiang Key Laboratory of Medical Epigenetics, School of Basic Medical Sciences, The Third People's Hospital of Deqing, Deqing Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Aiwei Wu
- Zhejiang Key Laboratory of Medical Epigenetics, School of Basic Medical Sciences, The Third People's Hospital of Deqing, Deqing Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Hu Wang
- Zhejiang Key Laboratory of Medical Epigenetics, School of Basic Medical Sciences, The Third People's Hospital of Deqing, Deqing Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
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3
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Alonso-Pérez V, Galant K, Boudia F, Robert E, Aid Z, Renou L, Barroca V, Devanand S, Babin L, Rouiller-Fabre V, Moison D, Busso D, Piton G, Metereau C, Abermil N, Ballerini P, Hirsch P, Haddad R, Martinovic J, Petit A, Lapillonne H, Brunet E, Mercher T, Pflumio F. Developmental interplay between transcriptional alterations and a targetable cytokine signaling dependency in pediatric ETO2::GLIS2 leukemia. Mol Cancer 2024; 23:204. [PMID: 39304903 DOI: 10.1186/s12943-024-02110-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Accepted: 09/02/2024] [Indexed: 09/22/2024] Open
Abstract
BACKGROUND Several fusion oncogenes showing a higher incidence in pediatric acute myeloid leukemia (AML) are associated with heterogeneous megakaryoblastic and other myeloid features. Here we addressed how developmental mechanisms influence human leukemogenesis by ETO2::GLIS2, associated with dismal prognosis. METHODS We created novel ETO2::GLIS2 models of leukemogenesis through lentiviral transduction and CRISPR-Cas9 gene editing of human fetal and post-natal hematopoietic stem/progenitor cells (HSPCs), performed in-depth characterization of ETO2::GLIS2 transformed cells through multiple omics and compared them to patient samples. This led to a preclinical assay using patient-derived-xenograft models to test a combination of two clinically-relevant molecules. RESULTS We showed that ETO2::GLIS2 expression in primary human fetal CD34+ hematopoietic cells led to more efficient in vivo leukemia development than expression in post-natal cells. Moreover, cord blood-derived leukemogenesis has a major dependency on the presence of human cytokines, including IL3 and SCF. Single cell transcriptomes revealed that this cytokine environment controlled two ETO2::GLIS2-transformed states that were also observed in primary patient cells. Importantly, this cytokine sensitivity may be therapeutically-exploited as combined MEK and BCL2 inhibition showed higher efficiency than individual molecules to reduce leukemia progression in vivo. CONCLUSIONS Our study uncovers an interplay between the cytokine milieu and transcriptional programs that extends a developmental window of permissiveness to transformation by the ETO2::GLIS2 AML fusion oncogene, controls the intratumoral cellular heterogeneity, and offers a ground-breaking therapeutical opportunity by a targeted combination strategy.
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Affiliation(s)
- Verónica Alonso-Pérez
- Commissariat À L'Energie Atomique Et Aux Energies Alternatives (CEA), Université Paris Cité, Institut National de La Santé Et de La Recherche Médicale (INSERM), Stabilité Génétique Cellules Souches Et Radiations, Fontenay-Aux-Roses, F-92260, France
- Université Paris-Saclay, INSERM, CEA, Stabilité Génétique Cellules Souches Et Radiations, Fontenay-Aux-Roses, F-92260, France
- Laboratoire Des Cellules Souches Hématopoïétiques Et Des Leucémies, Équipe Labellisée Ligue Contre Le Cancer, Equipe Niche Et Cancer Dans L'Hématopoïèse, Unité Mixte de Recherche (UMR) 1274 INSERM, CEA, 18 route du panorama, Fontenay-Aux Roses, F-92265, France
| | - Klaudia Galant
- Commissariat À L'Energie Atomique Et Aux Energies Alternatives (CEA), Université Paris Cité, Institut National de La Santé Et de La Recherche Médicale (INSERM), Stabilité Génétique Cellules Souches Et Radiations, Fontenay-Aux-Roses, F-92260, France
- Université Paris-Saclay, INSERM, CEA, Stabilité Génétique Cellules Souches Et Radiations, Fontenay-Aux-Roses, F-92260, France
- Laboratoire Des Cellules Souches Hématopoïétiques Et Des Leucémies, Équipe Labellisée Ligue Contre Le Cancer, Equipe Niche Et Cancer Dans L'Hématopoïèse, Unité Mixte de Recherche (UMR) 1274 INSERM, CEA, 18 route du panorama, Fontenay-Aux Roses, F-92265, France
| | - Fabien Boudia
- INSERM U1170, Gustave Roussy, Université Paris-Saclay, PEDIAC Program, Equipe Labellisée Ligue Contre Le Cancer, Villejuif, France
| | - Elie Robert
- INSERM U1170, Gustave Roussy, Université Paris-Saclay, PEDIAC Program, Equipe Labellisée Ligue Contre Le Cancer, Villejuif, France
| | - Zakia Aid
- INSERM U1170, Gustave Roussy, Université Paris-Saclay, PEDIAC Program, Equipe Labellisée Ligue Contre Le Cancer, Villejuif, France
| | - Laurent Renou
- Commissariat À L'Energie Atomique Et Aux Energies Alternatives (CEA), Université Paris Cité, Institut National de La Santé Et de La Recherche Médicale (INSERM), Stabilité Génétique Cellules Souches Et Radiations, Fontenay-Aux-Roses, F-92260, France
- Université Paris-Saclay, INSERM, CEA, Stabilité Génétique Cellules Souches Et Radiations, Fontenay-Aux-Roses, F-92260, France
- Laboratoire Des Cellules Souches Hématopoïétiques Et Des Leucémies, Équipe Labellisée Ligue Contre Le Cancer, Equipe Niche Et Cancer Dans L'Hématopoïèse, Unité Mixte de Recherche (UMR) 1274 INSERM, CEA, 18 route du panorama, Fontenay-Aux Roses, F-92265, France
| | - Vilma Barroca
- Commissariat À L'Energie Atomique Et Aux Energies Alternatives (CEA), Université Paris Cité, Institut National de La Santé Et de La Recherche Médicale (INSERM), Stabilité Génétique Cellules Souches Et Radiations, Fontenay-Aux-Roses, F-92260, France
- Université Paris-Saclay, INSERM, CEA, Stabilité Génétique Cellules Souches Et Radiations, Fontenay-Aux-Roses, F-92260, France
- Animal Experimentation Platform, IRCM, CEA, Fontenay-Aux-Roses, F-92260, France
| | - Saryiami Devanand
- Commissariat À L'Energie Atomique Et Aux Energies Alternatives (CEA), Université Paris Cité, Institut National de La Santé Et de La Recherche Médicale (INSERM), Stabilité Génétique Cellules Souches Et Radiations, Fontenay-Aux-Roses, F-92260, France
- Université Paris-Saclay, INSERM, CEA, Stabilité Génétique Cellules Souches Et Radiations, Fontenay-Aux-Roses, F-92260, France
- Animal Experimentation Platform, IRCM, CEA, Fontenay-Aux-Roses, F-92260, France
| | - Loélia Babin
- Laboratory of theGenome Dynamics in the Immune System, Équipe Labellisée Ligue Contre Le Cancer, Université Paris Cité, Université Paris-Saclay, INSERM UMR 1163, Institut Imagine, Paris, France
| | - Virginie Rouiller-Fabre
- Commissariat À L'Energie Atomique Et Aux Energies Alternatives (CEA), Université Paris Cité, Institut National de La Santé Et de La Recherche Médicale (INSERM), Stabilité Génétique Cellules Souches Et Radiations, Fontenay-Aux-Roses, F-92260, France
- Université Paris-Saclay, INSERM, CEA, Stabilité Génétique Cellules Souches Et Radiations, Fontenay-Aux-Roses, F-92260, France
| | - Delphine Moison
- Commissariat À L'Energie Atomique Et Aux Energies Alternatives (CEA), Université Paris Cité, Institut National de La Santé Et de La Recherche Médicale (INSERM), Stabilité Génétique Cellules Souches Et Radiations, Fontenay-Aux-Roses, F-92260, France
- Université Paris-Saclay, INSERM, CEA, Stabilité Génétique Cellules Souches Et Radiations, Fontenay-Aux-Roses, F-92260, France
| | - Didier Busso
- Commissariat À L'Energie Atomique Et Aux Energies Alternatives (CEA), Université Paris Cité, Institut National de La Santé Et de La Recherche Médicale (INSERM), Stabilité Génétique Cellules Souches Et Radiations, Fontenay-Aux-Roses, F-92260, France
- Université Paris-Saclay, INSERM, CEA, Stabilité Génétique Cellules Souches Et Radiations, Fontenay-Aux-Roses, F-92260, France
- Cigex Molecular Platform, IRCM, CEA, IBFJ, Fontenay-Aux-Roses, France
| | - Guillaume Piton
- Commissariat À L'Energie Atomique Et Aux Energies Alternatives (CEA), Université Paris Cité, Institut National de La Santé Et de La Recherche Médicale (INSERM), Stabilité Génétique Cellules Souches Et Radiations, Fontenay-Aux-Roses, F-92260, France
- Université Paris-Saclay, INSERM, CEA, Stabilité Génétique Cellules Souches Et Radiations, Fontenay-Aux-Roses, F-92260, France
- Cigex Molecular Platform, IRCM, CEA, IBFJ, Fontenay-Aux-Roses, France
| | - Christophe Metereau
- INSERM U1170, Gustave Roussy, Université Paris-Saclay, PEDIAC Program, Equipe Labellisée Ligue Contre Le Cancer, Villejuif, France
| | - Nassera Abermil
- Centre de Recherche Saint-Antoine, CRSA, SIRIC CURAMUS, Hôpital Saint-Antoine, Service d'Hématologie Biologique, Sorbonne Université, 75012, Paris, France
| | - Paola Ballerini
- Department of Pediatric Hematology-Oncology, Hôpital Armand Trousseau, AP-HP, Paris, France
| | - Pierre Hirsch
- Centre de Recherche Saint-Antoine, CRSA, SIRIC CURAMUS, Hôpital Saint-Antoine, Service d'Hématologie Biologique, Sorbonne Université, 75012, Paris, France
| | - Rima Haddad
- Commissariat À L'Energie Atomique Et Aux Energies Alternatives (CEA), Université Paris Cité, Institut National de La Santé Et de La Recherche Médicale (INSERM), Stabilité Génétique Cellules Souches Et Radiations, Fontenay-Aux-Roses, F-92260, France
- Université Paris-Saclay, INSERM, CEA, Stabilité Génétique Cellules Souches Et Radiations, Fontenay-Aux-Roses, F-92260, France
- Laboratoire Des Cellules Souches Hématopoïétiques Et Des Leucémies, Équipe Labellisée Ligue Contre Le Cancer, Equipe Niche Et Cancer Dans L'Hématopoïèse, Unité Mixte de Recherche (UMR) 1274 INSERM, CEA, 18 route du panorama, Fontenay-Aux Roses, F-92265, France
| | - Jelena Martinovic
- Unit of Fetal Pathology, Hôpital Antoine Beclère, AP-HP, Clamart, France
| | - Arnaud Petit
- Department of Pediatric Hematology-Oncology, Hôpital Armand Trousseau, AP-HP, Paris, France
| | - Hélène Lapillonne
- Department of Pediatric Hematology-Oncology, Hôpital Armand Trousseau, AP-HP, Paris, France
| | - Erika Brunet
- Laboratory of theGenome Dynamics in the Immune System, Équipe Labellisée Ligue Contre Le Cancer, Université Paris Cité, Université Paris-Saclay, INSERM UMR 1163, Institut Imagine, Paris, France
| | - Thomas Mercher
- INSERM U1170, Gustave Roussy, Université Paris-Saclay, PEDIAC Program, Equipe Labellisée Ligue Contre Le Cancer, Villejuif, France.
- OPALE Carnot Institute, The Organization for Partnerships in Leukemia, Paris, France.
| | - Françoise Pflumio
- Commissariat À L'Energie Atomique Et Aux Energies Alternatives (CEA), Université Paris Cité, Institut National de La Santé Et de La Recherche Médicale (INSERM), Stabilité Génétique Cellules Souches Et Radiations, Fontenay-Aux-Roses, F-92260, France.
- Université Paris-Saclay, INSERM, CEA, Stabilité Génétique Cellules Souches Et Radiations, Fontenay-Aux-Roses, F-92260, France.
- Laboratoire Des Cellules Souches Hématopoïétiques Et Des Leucémies, Équipe Labellisée Ligue Contre Le Cancer, Equipe Niche Et Cancer Dans L'Hématopoïèse, Unité Mixte de Recherche (UMR) 1274 INSERM, CEA, 18 route du panorama, Fontenay-Aux Roses, F-92265, France.
- OPALE Carnot Institute, The Organization for Partnerships in Leukemia, Paris, France.
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Fobare S, Sharpe C, Quinn K, Bryant K, Miles LA, Bowman RL, Cheney C, Furby C, Long M, Fyock K, Wronowski B, Lerma JR, Mullaney A, Mrózek K, Nicolet D, Sesterhenn T, Johnstone ME, Rai SN, Pasare C, Zimmermann N, Carroll AJ, Stone RM, Wang ES, Kolitz JE, Powell BL, Perentesis JP, Eisfeld AK, Hertlein E, Byrd JC. PTPN11 Mutation Clonal Hierarchy in Acute Myeloid Leukemia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.18.612239. [PMID: 39345464 PMCID: PMC11429687 DOI: 10.1101/2024.09.18.612239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Mutations in protein tyrosine phosphatase non-receptor type 11 ( PTPN11 ) have been considered late acquired mutations in acute myeloid leukemia (AML) development. To interrogate the ontogeny of PTPN11 mutations, we utilized single-cell DNA sequencing and identified that PTPN11 mutations can occur as initiating events in some AML patients when accompanied by strong oncogenic drivers, commonly NPM1 mutations. The co-driver role of PTPN11 mutations was confirmed in a novel murine model that exhibits an AML phenotype with early expansion of a diverse set of variably differentiated myeloid cells that engrafted into immunodeficient and immunocompetent mice. This immune diversity was reconstituted from early precursor cells when engrafted into immunodeficient mice. Moreover, immune diversity was also observed in the blast component of patient samples with NPM1 and PTPN11 mutations, providing novel antigen targets for immune based approaches in this subset of AML that is resistant to multiple targeted therapies.
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Zhou J, Zhang N, Zuo Y, Xu F, Cheng L, Fu Y, Yang F, Shu M, Zhou M, Zou W, Zhang S. Glutamine metabolism-related genes predict the prognostic risk of acute myeloid leukemia and stratify patients by subtype analysis. Hereditas 2024; 161:35. [PMID: 39300580 DOI: 10.1186/s41065-024-00338-8] [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: 05/10/2024] [Accepted: 09/11/2024] [Indexed: 09/22/2024] Open
Abstract
BACKGROUND Acute myeloid leukemia (AML) is a genetically heterogeneous disease in which glutamine (Gln) contributes to AML progression. Therefore, this study aimed to identify potential prognostic biomarkers for AML based on Gln metabolism-related genes. METHODS Gln-related genes that were differentially expressed between Cancer Genome Atlas-based AML and normal samples were analyzed using the limma package. Univariate, least absolute shrinkage, selection operators, and stepwise Cox regression analyses were used to identify prognostic signatures. Risk score-based prognostic and nomogram models were constructed to predict the prognostic risk of AML. Subsequently, consistent cluster analysis was performed to stratify patients into different subtypes, and subtype-related module genes were screened using weighted gene co-expression network analysis. RESULTS Through a series of regression analyses, HGF, ANGPTL3, MB, F2, CALR, EIF4EBP1, EPHX1, and PDHA1 were identified as potential prognostic biomarkers of AML. Prognostic and nomogram models constructed based on these genes could significantly differentiate between high- and low-risk AML with high predictive accuracy. The eight-signature also stratified patients with AML into two subtypes, among which Cluster 2 was prone to a high risk of AML prognosis. These two clusters exhibited different immune profiles. Of the subtype-related module genes, the HOXA and HOXB family genes may be genetic features of AML subtypes. CONCLUSION Eight Gln metabolism-related genes were identified as potential biomarkers of AML to predict prognostic risk. The molecular subtypes clustered by these genes enabled prognostic risk stratification.
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Affiliation(s)
- Jie Zhou
- Department of Hematology, Deyang People's Hospital, No. 173 Taishan North Road, Section 1, Jingyang District, Deyang, 618000, Sichuan, China.
| | - Na Zhang
- Department of Hematology, Deyang People's Hospital, No. 173 Taishan North Road, Section 1, Jingyang District, Deyang, 618000, Sichuan, China
| | - Yan Zuo
- Department of Hematology, Deyang People's Hospital, No. 173 Taishan North Road, Section 1, Jingyang District, Deyang, 618000, Sichuan, China
| | - Feng Xu
- Department of Hematology, Deyang People's Hospital, No. 173 Taishan North Road, Section 1, Jingyang District, Deyang, 618000, Sichuan, China
| | - Lihua Cheng
- Department of Hematology, Deyang People's Hospital, No. 173 Taishan North Road, Section 1, Jingyang District, Deyang, 618000, Sichuan, China
| | - Yuanyuan Fu
- Department of Hematology, Deyang People's Hospital, No. 173 Taishan North Road, Section 1, Jingyang District, Deyang, 618000, Sichuan, China
| | - Fudong Yang
- Department of Hematology, Deyang People's Hospital, No. 173 Taishan North Road, Section 1, Jingyang District, Deyang, 618000, Sichuan, China
| | - Min Shu
- Department of Hematology, Deyang People's Hospital, No. 173 Taishan North Road, Section 1, Jingyang District, Deyang, 618000, Sichuan, China
| | - Mi Zhou
- Department of Hematology, Deyang People's Hospital, No. 173 Taishan North Road, Section 1, Jingyang District, Deyang, 618000, Sichuan, China
| | - Wenting Zou
- Department of Hematology, Deyang People's Hospital, No. 173 Taishan North Road, Section 1, Jingyang District, Deyang, 618000, Sichuan, China
| | - Shengming Zhang
- Department of health management, Guangdong Second Provincial General Hospital, Guangzhou, 510317, Guangdong, China.
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Lints R, Walker CA, Delfi O, Prouse M, PohLui De Silva M, Bohlander SK, Wood AC. Mutational cooperativity of RUNX1::RUNX1T1 isoform 9a and oncogenic NRAS in zebrafish myeloid leukaemia. Biol Open 2024; 13:bio060523. [PMID: 39177514 PMCID: PMC11381922 DOI: 10.1242/bio.060523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Accepted: 08/01/2024] [Indexed: 08/24/2024] Open
Abstract
RUNX1::RUNX1T1 (R::RT1) acute myeloid leukaemia (AML) remains a clinical challenge, and further research is required to model and understand leukaemogenesis. Previous zebrafish R::RT1 models were hampered by embryonic lethality and low penetrance of the malignant phenotype. Here, we overcome this by developing an adult zebrafish model in which the human R::RT1 isoform 9a is co-expressed with the frequently co-occurring oncogenic NRASG12D mutation in haematopoietic stem and progenitor cells (HSPCs), using the Runx1+23 enhancer. Approximately 50% of F0 9a+NRASG12D transgenic zebrafish developed signs of haematological disease between 5 and 14 months, with 27% exhibiting AML-like pathology: myeloid precursor expansion, erythrocyte reduction, kidney marrow hypercellularity and the presence of blasts. Moreover, only 9a+NRASG12D transplant recipients developed leukaemia with high rates of mortality within 40 days, inferring the presence of leukaemia stem cells. These leukaemic features were rare or not observed in animals expressing either the NRAS or 9a oncogenes alone, suggesting 9a and NRAS cooperation drives leukaemogenesis. This novel adult AML zebrafish model provides a powerful new tool for investigating the basis of R::RT1 - NRAS cooperativity with the potential to uncover new therapeutic targets.
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Affiliation(s)
- Robyn Lints
- Leukaemia and Blood Cancer Research Unit, Department of Molecular Medicine and Pathology, University of Auckland, Auckland 1023, New Zealand
| | - Christina A Walker
- Leukaemia and Blood Cancer Research Unit, Department of Molecular Medicine and Pathology, University of Auckland, Auckland 1023, New Zealand
| | - Omid Delfi
- Leukaemia and Blood Cancer Research Unit, Department of Molecular Medicine and Pathology, University of Auckland, Auckland 1023, New Zealand
| | - Matthew Prouse
- Leukaemia and Blood Cancer Research Unit, Department of Molecular Medicine and Pathology, University of Auckland, Auckland 1023, New Zealand
| | | | - Stefan K Bohlander
- Leukaemia and Blood Cancer Research Unit, Department of Molecular Medicine and Pathology, University of Auckland, Auckland 1023, New Zealand
| | - Andrew C Wood
- Leukaemia and Blood Cancer Research Unit, Department of Molecular Medicine and Pathology, University of Auckland, Auckland 1023, New Zealand
- Starship Child Health, Starship Blood and Cancer Centre, Auckland 1023, New Zealand
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Cull AH, Kent DG, Warren AJ. Emerging genetic technologies informing personalized medicine in Shwachman-Diamond syndrome and other inherited BMF disorders. Blood 2024; 144:931-939. [PMID: 38905596 DOI: 10.1182/blood.2023019986] [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: 04/02/2024] [Revised: 06/11/2024] [Accepted: 06/11/2024] [Indexed: 06/23/2024] Open
Abstract
ABSTRACT Ribosomopathy Shwachman-Diamond syndrome (SDS) is a rare autosomal recessive inherited bone marrow failure syndrome (IBMFS) caused by mutations in the Shwachman-Bodian-Diamond syndrome gene, which is associated with an increased risk of myeloid malignancy. Tracking how hematopoietic stem cell (HSC) clonal dynamics change over time, assessing whether somatic genetic rescue mechanisms affect these dynamics, and mapping out when leukemic driver mutations are acquired is important to understand which individuals with SDS may go on to develop leukemia. In this review, we discuss how new technologies that allow researchers to map mutations at the level of single HSC clones are generating important insights into genetic rescue mechanisms and their relative risk for driving evolution to leukemia, and how these data can inform the future development of personalized medicine approaches in SDS and other IBMFSs.
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Affiliation(s)
- Alyssa H Cull
- Department of Biology, Centre for Blood Research, York Biomedical Research Institute, University of York, York, United Kingdom
| | - David G Kent
- Department of Biology, Centre for Blood Research, York Biomedical Research Institute, University of York, York, United Kingdom
| | - Alan J Warren
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust-Medical Research Council Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, United Kingdom
- Department of Hematology, School of Clinical Medicine, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, United Kingdom
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8
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Fischer A, Hernández-Rodríguez B, Mulet-Lazaro R, Nuetzel M, Hölzl F, van Herk S, Kavelaars FG, Stanewsky H, Ackermann U, Niang AH, Diaz N, Reuschel E, Strieder N, Hernández-López I, Valk PJM, Vaquerizas JM, Rehli M, Delwel R, Gebhard C. STAG2 mutations reshape the cohesin-structured spatial chromatin architecture to drive gene regulation in acute myeloid leukemia. Cell Rep 2024; 43:114498. [PMID: 39084219 DOI: 10.1016/j.celrep.2024.114498] [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: 12/11/2023] [Revised: 05/24/2024] [Accepted: 06/27/2024] [Indexed: 08/02/2024] Open
Abstract
Cohesin shapes the chromatin architecture, including enhancer-promoter interactions. Its components, especially STAG2, but not its paralog STAG1, are frequently mutated in myeloid malignancies. To elucidate the underlying mechanisms of leukemogenesis, we comprehensively characterized genetic, transcriptional, and chromatin conformational changes in acute myeloid leukemia (AML) patient samples. Specific loci displayed altered cohesin occupancy, gene expression, and local chromatin activation, which were not compensated by the remaining STAG1-cohesin. These changes could be linked to disrupted spatial chromatin looping in cohesin-mutated AMLs. Complementary depletion of STAG2 or STAG1 in primary human hematopoietic progenitors (HSPCs) revealed effects resembling STAG2-mutant AML-specific changes following STAG2 knockdown, not invoked by the depletion of STAG1. STAG2-deficient HSPCs displayed impaired differentiation capacity and maintained HSPC-like gene expression. This work establishes STAG2 as a key regulator of chromatin contacts, gene expression, and differentiation in the hematopoietic system and identifies candidate target genes that may be implicated in human leukemogenesis.
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MESH Headings
- Humans
- Cohesins
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Leukemia, Myeloid, Acute/metabolism
- Cell Cycle Proteins/metabolism
- Cell Cycle Proteins/genetics
- Chromatin/metabolism
- Chromosomal Proteins, Non-Histone/metabolism
- Chromosomal Proteins, Non-Histone/genetics
- Mutation/genetics
- Hematopoietic Stem Cells/metabolism
- Cell Differentiation/genetics
- Gene Expression Regulation, Leukemic
- Antigens, Nuclear/metabolism
- Antigens, Nuclear/genetics
- Nuclear Proteins
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Affiliation(s)
- Alexander Fischer
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany; Leibniz Institute for Immunotherapy, Regensburg, Germany
| | | | - Roger Mulet-Lazaro
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Margit Nuetzel
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Fabian Hölzl
- Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Stanley van Herk
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - François G Kavelaars
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Hanna Stanewsky
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Ute Ackermann
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Amadou H Niang
- Regulatory Genomics, Max Plank Institute for Molecular Medicine, Münster, Germany
| | - Noelia Diaz
- Regulatory Genomics, Max Plank Institute for Molecular Medicine, Münster, Germany
| | - Edith Reuschel
- Department of Obstetrics and Gynecology, Hospital St. Hedwig of the Order of St. John, Regensburg, Germany
| | | | | | - Peter J M Valk
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Juan M Vaquerizas
- Regulatory Genomics, Max Plank Institute for Molecular Medicine, Münster, Germany; Department of Developmental Epigenomics, MRC London Institute of Medical Sciences, London, UK; Institute of Clinical Sciences, Imperial College London, London, UK
| | - Michael Rehli
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany; Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Ruud Delwel
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands; Oncode Institute, Utrecht, the Netherlands
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9
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Wong TN, Mychalowych A, Feldpausch ER, Carson A, Karpova D, Link DC. The Clonal Hematopoiesis-associated Gene Srcap Plays an Essential Role in Hematopoiesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.16.607812. [PMID: 39229096 PMCID: PMC11370474 DOI: 10.1101/2024.08.16.607812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Somatic mutations arising in hematopoietic stem cells (HSCs) may provide the latter with a fitness advantage, allowing the mutant HSC to clonally expand. Such mutations have been recurrently identified in the chromatin modifier, SRCAP, in both non-malignant and leukemic clones, suggesting that this gene plays a significant role in hematopoiesis. We generated a conditional Srcap loss of function murine model and determined the consequences of hematopoietic-specific loss of this gene. We show that Srcap is essential for normal fetal liver erythropoiesis and monocytopoiesis. In Srcap deficient fetal livers, the number of phenotypic HSCs is similar to that of controls, but these HSCs exhibit a profound repopulating defect. Likewise, conditional deletion of Srcap during adult hematopoiesis results in a rapid loss of HSCs. Loss of Srcap is associated with evidence of increased DNA damage in HSCs and lineage-restricted progenitors as assessed by y-H2AX expression. Consistent with this finding, we observed strong transcriptional upregulation of the p53 pathway in Srcap deficient erythroid precursors. Collectively our data highlight the importance of Srcap in maintaining HSC function and supporting hematopoietic differentiation and suggests that it plays an essential role in maintaining genomic integrity.
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Affiliation(s)
- Terrence N Wong
- Division of Hematology-Oncology, University of Michigan, Ann Arbor, Michigan
| | - Anna Mychalowych
- Division of Hematology-Oncology, University of Michigan, Ann Arbor, Michigan
| | - Ellie R Feldpausch
- Division of Hematology-Oncology, University of Michigan, Ann Arbor, Michigan
| | - Alexander Carson
- Division of Hematology-Oncology, University of Michigan, Ann Arbor, Michigan
| | - Darja Karpova
- Division of Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Daniel C Link
- Division of Oncology, Washington University School of Medicine, St. Louis, Missouri
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10
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Li HD, Chen SS, Ding J, Zhang CL, Qiu HY, Xia XX, Yang J, Wang XR. Exploration of ETV6::ABL1-positive AML with concurrent NPM1 and FLT3-ITD mutations. Ann Hematol 2024:10.1007/s00277-024-05917-3. [PMID: 39105739 DOI: 10.1007/s00277-024-05917-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Accepted: 07/26/2024] [Indexed: 08/07/2024]
Abstract
ETV6::ABL1 is a rare fusion gene that found in MPN, ALL, and AML. It has a complex and diverse formation mechanism due to the reciprocal orientations of the ETV6 and ABL1 genes relative to the centromeres. NPM1 is frequently mutated in adult AML, often accompanied by FLT3-ITD, which suggests molecular synergisms in AML pathogenesis. Previous reports on ETV6::ABL1 mostly focus on FLT3-ITD. In this study, we present a case of AML with ETV6::ABL1, along with NPM1 and FLT3-ITD. The patient showed a rapid increase in primitive cells at the initial stage, along with the presence of immature granulocytes and erythrocytes. Through cytogenetic analysis, fluorescence in situ hybridization (FISH), and RNA-seq, we elucidated the mechanism behind the formation of the ETV6::ABL1 fusion gene. Despite conventional chemotherapy failure and rapid tumor proliferation, we attempted to add FLT3 inhibitor sorafenib to the treatment, along with chemotherapy bridging to haploidentical transplantation. After haplo-HSCT, a combination of sorafenib and dasatinib was administered as maintenance therapy. The patient achieved complete remission (CR) and maintained it for 11 months. The intricate genetic landscape observed in this case presents diagnostic dilemmas and therapeutic challenges, emphasizing the importance of a comprehensive understanding of its implications for disease classification, risk stratification, and treatment selection.
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Affiliation(s)
- Hui-Dan Li
- Clinical Laboratory Medicine Center, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200080, China
| | - Si-Si Chen
- Clinical Research Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Jing Ding
- Clinical Laboratory Medicine Center, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200080, China
| | - Chun-Ling Zhang
- Clinical Laboratory Medicine Center, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200080, China
| | - Hui-Yin Qiu
- Department of Hematology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Xin-Xin Xia
- Department of Hematology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Jun Yang
- Department of Hematology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China.
| | - Xiao-Rui Wang
- Clinical Laboratory Medicine Center, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200080, China.
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11
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Berry DK, Gillis N, Padron E, Moore C, Barton LV, Gewandter KR, Haskins CG, Knepper TC. Interpretation of ambiguous TP53 test results: Mosaicism, clonal hematopoiesis, and variants of uncertain significance. J Genet Couns 2024; 33:916-926. [PMID: 37715966 DOI: 10.1002/jgc4.1789] [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: 04/03/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/18/2023]
Abstract
The increased use of next-generation sequencing has led to the detection of pathogenic TP53 variants in the germline setting in patients without a personal or family history consistent with Li-Fraumeni syndrome (LFS). These variants can represent low-penetrance LFS, mosaic LFS, or clonal hematopoiesis of indeterminate potential. Additionally, TP53 variants of uncertain significance can be detected in patients with a history suspicious for LFS. The interpretation of the significance of these variants can be challenging but is crucial for an accurate diagnosis and appropriate medical management. This retrospective case review provides illustrative examples of the interpretation of challenging TP53 results through multidisciplinary expertise and use of a flowchart. The authors describe eight patients with TP53 variants associated with ambiguous diagnoses and, for each case, describe how the results were interpreted and the medical care that was implemented. This report presents illustrative cases to help guide clinicians to reach definitive diagnoses for patients when confronted with TP53 variants that are inconsistent with the clinical picture and to add to the body of literature regarding interpretation and medical management of TP53 variants discovered on germline testing.
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Affiliation(s)
- Darcy K Berry
- Department of Individualized Cancer Management, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Nancy Gillis
- Department of Cancer Epidemiology, Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
- Department of Malignant Hematology, Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Eric Padron
- Department of Malignant Hematology, Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Colin Moore
- Department of Individualized Cancer Management, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Laura V Barton
- Department of Individualized Cancer Management, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Kathleen R Gewandter
- Department of Individualized Cancer Management, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Carolyn G Haskins
- Department of Individualized Cancer Management, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Todd C Knepper
- Department of Individualized Cancer Management, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
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12
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Jakobsen NA, Turkalj S, Zeng AGX, Stoilova B, Metzner M, Rahmig S, Nagree MS, Shah S, Moore R, Usukhbayar B, Angulo Salazar M, Gafencu GA, Kennedy A, Newman S, Kendrick BJL, Taylor AH, Afinowi-Luitz R, Gundle R, Watkins B, Wheway K, Beazley D, Murison A, Aguilar-Navarro AG, Flores-Figueroa E, Dakin SG, Carr AJ, Nerlov C, Dick JE, Xie SZ, Vyas P. Selective advantage of mutant stem cells in human clonal hematopoiesis is associated with attenuated response to inflammation and aging. Cell Stem Cell 2024; 31:1127-1144.e17. [PMID: 38917807 DOI: 10.1016/j.stem.2024.05.010] [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: 06/25/2023] [Revised: 01/29/2024] [Accepted: 05/30/2024] [Indexed: 06/27/2024]
Abstract
Clonal hematopoiesis (CH) arises when hematopoietic stem cells (HSCs) acquire mutations, most frequently in the DNMT3A and TET2 genes, conferring a competitive advantage through mechanisms that remain unclear. To gain insight into how CH mutations enable gradual clonal expansion, we used single-cell multi-omics with high-fidelity genotyping on human CH bone marrow (BM) samples. Most of the selective advantage of mutant cells occurs within HSCs. DNMT3A- and TET2-mutant clones expand further in early progenitors, while TET2 mutations accelerate myeloid maturation in a dose-dependent manner. Unexpectedly, both mutant and non-mutant HSCs from CH samples are enriched for inflammatory and aging transcriptomic signatures, compared with HSCs from non-CH samples, revealing a non-cell-autonomous effect. However, DNMT3A- and TET2-mutant HSCs have an attenuated inflammatory response relative to wild-type HSCs within the same sample. Our data support a model whereby CH clones are gradually selected because they are resistant to the deleterious impact of inflammation and aging.
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Affiliation(s)
- Niels Asger Jakobsen
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Sven Turkalj
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Andy G X Zeng
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Bilyana Stoilova
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Marlen Metzner
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Susann Rahmig
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Murtaza S Nagree
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Sayyam Shah
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Rachel Moore
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Batchimeg Usukhbayar
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Mirian Angulo Salazar
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Grigore-Aristide Gafencu
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Alison Kennedy
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Simon Newman
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK; Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Benjamin J L Kendrick
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK; Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Adrian H Taylor
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK; Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Rasheed Afinowi-Luitz
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK; Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Roger Gundle
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK; Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Bridget Watkins
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK
| | - Kim Wheway
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK
| | - Debra Beazley
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK
| | - Alex Murison
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Alicia G Aguilar-Navarro
- Unidad de Investigación Médica en Enfermedades Oncológicas, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Eugenia Flores-Figueroa
- Unidad de Investigación Médica en Enfermedades Oncológicas, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Stephanie G Dakin
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK
| | - Andrew J Carr
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK; Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Claus Nerlov
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Stephanie Z Xie
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Paresh Vyas
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK; Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
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13
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Petrone G, Turker I, Natarajan P, Bolton KL. Clinical and Therapeutic Implications of Clonal Hematopoiesis. Annu Rev Genomics Hum Genet 2024; 25:329-351. [PMID: 39190914 DOI: 10.1146/annurev-genom-120722-100409] [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] [Indexed: 08/29/2024]
Abstract
Clonal hematopoiesis (CH) is an age-related process whereby hematopoietic stem and progenitor cells (HSPCs) acquire mutations that lead to a proliferative advantage and clonal expansion. The most commonly mutated genes are epigenetic regulators, DNA damage response genes, and splicing factors, which are essential to maintain functional HSPCs and are frequently involved in the development of hematologic malignancies. Established risk factors for CH, including age, prior cytotoxic therapy, and smoking, increase the risk of acquiring CH and/or may increase CH fitness. CH has emerged as a novel risk factor in many age-related diseases, such as hematologic malignancies, cardiovascular disease, diabetes, and autoimmune disorders, among others. Future characterization of the mechanisms driving CH evolution will be critical to develop preventative and therapeutic approaches.
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Affiliation(s)
- Giulia Petrone
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA;
| | - Isik Turker
- Division of Cardiology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Pradeep Natarajan
- Cardiovascular Research Center and Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Kelly L Bolton
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA;
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14
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Wang S, Liu Y, Zhao X, Wang X, Lou J, Jin P, Zhang Y, Yu J, Wang K. RUNX1::ETO and CBFβ::MYH11 converge on aberrant activation of BCAT1 to confer a therapeutic vulnerability in core-binding factor-acute myeloid leukaemia. Br J Haematol 2024; 205:552-567. [PMID: 38802066 DOI: 10.1111/bjh.19565] [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: 02/14/2024] [Accepted: 05/15/2024] [Indexed: 05/29/2024]
Abstract
Effectively targeting transcription factors in therapeutic interventions remains challenging, especially in core-binding factor-acute myeloid leukaemia (CBF-AML) characterized by RUNX1::ETO and CBFβ::MYH11 fusions. However, recent studies have drawn attention towards aberrant amino acid metabolisms as actionable therapeutic targets. Here, by integrating the expression profile and genetic makeup in AML cohort, we found higher BCAT1 expression in CBF-AML patients compared with other subtypes. Metabolic profiling revealed that high BCAT1 expression led to reprogrammed branch amino acid metabolism in CBF-AML and was associated with sphingolipid pathway relating to the fitness of leukaemia cells, supported by transcriptomic profiling. Mechanistically, we demonstrated in cell lines and primary patient samples that BCAT1 was directly activated by RUNX1::ETO and CBFβ::MYH11 fusion proteins similarly in a RUNX1-dependent manner through rewiring chromatin conformation at the BCAT1 gene locus. Furthermore, BCAT1 inhibition resulted in blunted cell cycle, enhanced apoptosis and myeloid differentiation of CBF-AML cells in vitro, and alleviated leukaemia burden and prolonged survival in vivo. Importantly, pharmacological inhibition of BCAT1 using the specific inhibitor Gabapentin demonstrated therapeutic effects, as evidenced by delayed leukaemia progression and improved survival in vivo. In conclusion, our study uncovers BCAT1 as a genetic vulnerability and a promising targeted therapeutic opportunity for CBF-AML.
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MESH Headings
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/pathology
- Core Binding Factor Alpha 2 Subunit/genetics
- Core Binding Factor Alpha 2 Subunit/metabolism
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Animals
- Core Binding Factor beta Subunit/genetics
- Core Binding Factor beta Subunit/metabolism
- Mice
- Gene Expression Regulation, Leukemic
- Cell Line, Tumor
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Affiliation(s)
- Siyang Wang
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yabin Liu
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Xujie Zhao
- School of Life Sciences and Technology, Advanced Institute for Life and Health, Zhongda Hospital, Southeast University, Nanjing, China
| | - Xiaoling Wang
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Reproductive Medical Center, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiacheng Lou
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Department of Neurosurgery, Second Hospital of Dalian Medical University, Dalian, China
| | - Peng Jin
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi Zhang
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jinyi Yu
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kankan Wang
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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15
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Pendse S, Loeffler D. Decoding Clonal Hematopoiesis: Emerging Themes and Novel Mechanistic Insights. Cancers (Basel) 2024; 16:2634. [PMID: 39123361 PMCID: PMC11311828 DOI: 10.3390/cancers16152634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 07/22/2024] [Accepted: 07/22/2024] [Indexed: 08/12/2024] Open
Abstract
Clonal hematopoiesis (CH), the relative expansion of mutant clones, is derived from hematopoietic stem cells (HSCs) with acquired somatic or cytogenetic alterations that improve cellular fitness. Individuals with CH have a higher risk for hematological and non-hematological diseases, such as cardiovascular disease, and have an overall higher mortality rate. Originally thought to be restricted to a small fraction of elderly people, recent advances in single-cell sequencing and bioinformatics have revealed that CH with multiple expanded mutant clones is universal in the elderly population. Just a few years ago, phylogenetic reconstruction across the human lifespan and novel sensitive sequencing techniques showed that CH can start earlier in life, decades before it was thought possible. These studies also suggest that environmental factors acting through aberrant inflammation might be a common theme promoting clonal expansion and disease progression. However, numerous aspects of this phenomenon remain to be elucidated and the precise mechanisms, context-specific drivers, and pathways of clonal expansion remain to be established. Here, we review our current understanding of the cellular mechanisms driving CH and specifically focus on how pro-inflammatory factors affect normal and mutant HSC fates to promote clonal selection.
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Affiliation(s)
- Shalmali Pendse
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Comprehensive Cancer Center, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pathology & Laboratory Medicine, The University of Tennessee, Memphis, TN 37996, USA
| | - Dirk Loeffler
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Comprehensive Cancer Center, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Pathology & Laboratory Medicine, The University of Tennessee, Memphis, TN 37996, USA
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16
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Zhu R, Shirley CM, Chu SH, Li L, Nguyen BH, Seo J, Wu M, Seale T, Duffield AS, Staudt LM, Levis M, Hu Y, Small D. Inhibition of NOTCH4 sensitizes FLT3/ITD acute myeloid leukemia cells to FLT3 tyrosine kinase inhibition. Leukemia 2024; 38:1581-1591. [PMID: 38811818 DOI: 10.1038/s41375-024-02292-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 05/13/2024] [Accepted: 05/16/2024] [Indexed: 05/31/2024]
Abstract
Internal tandem duplication mutations of FLT3 (FLT3/ITD) confer poor prognosis in AML. FLT3 tyrosine kinase inhibitors (TKIs) alone have limited and transient clinical efficacy thus calling for new targets for more effective combination therapy. In a loss-of-function RNAi screen, we identified NOTCH4 as one such potential target whose inhibition proved cytotoxic to AML cells, and also sensitized them to FLT3 inhibition. Further investigation found increased NOTCH4 expression in FLT3/ITD AML cell lines and primary patient samples. Inhibition of NOTCH4 by shRNA knockdown, CRISPR-Cas9-based knockout or γ-secretase inhibitors synergized with FLT3 TKIs to kill FLT3/ITD AML cells in vitro. NOTCH4 inhibition sensitized TKI-resistant FLT3/ITD cells to FLT3 TKI inhibition. The combination reduced phospho-ERK and phospho-AKT, indicating inhibition of MAPK and PI3K/AKT signaling pathways. It also led to changes in expression of genes involved in regulating cell cycling, DNA repair and transcription. A patient-derived xenograft model showed that the combination reduced both the level of leukemic involvement of primary human FLT3/ITD AML cells and their ability to engraft secondary recipients. In summary, these results demonstrate that NOTCH4 inhibition synergizes with FLT3 TKIs to eliminate FLT3/ITD AML cells, providing a new therapeutic target for AML with FLT3/ITD mutations.
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MESH Headings
- Humans
- fms-Like Tyrosine Kinase 3/genetics
- fms-Like Tyrosine Kinase 3/antagonists & inhibitors
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Leukemia, Myeloid, Acute/metabolism
- Animals
- Protein Kinase Inhibitors/pharmacology
- Protein Kinase Inhibitors/therapeutic use
- Mice
- Receptor, Notch4/genetics
- Xenograft Model Antitumor Assays
- Mutation
- Cell Line, Tumor
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Signal Transduction/drug effects
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Affiliation(s)
- Ruiqi Zhu
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Courtney M Shirley
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - S Haihua Chu
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Beam Therapeutics, Cambridge, MA, USA
| | - Li Li
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Bao H Nguyen
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jaesung Seo
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Min Wu
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tessa Seale
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Amy S Duffield
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Louis M Staudt
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mark Levis
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yu Hu
- Department of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Donald Small
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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17
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Mack T, Vlasschaert C, von Beck K, Silver AJ, Heimlich JB, Poisner H, Condon HR, Ulloa J, Sochacki AL, Spaulding TP, Kishtagari A, Bejan CA, Xu Y, Savona MR, Jones A, Bick AG. Cost-Effective and Scalable Clonal Hematopoiesis Assay Provides Insight into Clonal Dynamics. J Mol Diagn 2024; 26:563-573. [PMID: 38588769 DOI: 10.1016/j.jmoldx.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/06/2024] [Accepted: 03/13/2024] [Indexed: 04/10/2024] Open
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP) is a common age-related phenomenon in which hematopoietic stem cells acquire mutations in a select set of genes commonly mutated in myeloid neoplasia which then expand clonally. Current sequencing assays to detect CHIP mutations are not optimized for the detection of these variants and can be cost-prohibitive when applied to large cohorts or to serial sequencing. In this study, an affordable (approximately US $8 per sample), accurate, and scalable sequencing assay for CHIP is introduced and validated. The efficacy of the assay was demonstrated by identifying CHIP mutations in a cohort of 456 individuals with DNA collected at multiple time points in Vanderbilt University's biobank and quantifying clonal expansion rates over time. A total of 101 individuals with CHIP/clonal cytopenia of undetermined significance were identified, and individual-level clonal expansion rate was calculated using the variant allele fraction at both time points. Differences in clonal expansion rate by driver gene were observed, but there was also significant individual-level heterogeneity, emphasizing the multifactorial nature of clonal expansion. Additionally, mutation co-occurrence and clonal competition between multiple driver mutations were explored.
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Affiliation(s)
- Taralynn Mack
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, Tennessee
| | | | - Kelly von Beck
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Alexander J Silver
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - J Brett Heimlich
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Hannah Poisner
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Henry R Condon
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jessica Ulloa
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Andrew L Sochacki
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Travis P Spaulding
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Ashwin Kishtagari
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Cosmin A Bejan
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Yaomin Xu
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Michael R Savona
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee; Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee; Center for Immunobiology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Angela Jones
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Alexander G Bick
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, Tennessee; Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee.
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18
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Wells C, Robertson T, Sheth P, Abraham S. How aging influences the gut-bone marrow axis and alters hematopoietic stem cell regulation. Heliyon 2024; 10:e32831. [PMID: 38984298 PMCID: PMC11231543 DOI: 10.1016/j.heliyon.2024.e32831] [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: 03/11/2024] [Revised: 06/03/2024] [Accepted: 06/10/2024] [Indexed: 07/11/2024] Open
Abstract
The gut microbiome has come to prominence across research disciplines, due to its influence on major biological systems within humans. Recently, a relationship between the gut microbiome and hematopoietic system has been identified and coined the gut-bone marrow axis. It is well established that the hematopoietic system and gut microbiome separately alter with age; however, the relationship between these changes and how these systems influence each other demands investigation. Since the hematopoietic system produces immune cells that help govern commensal bacteria, it is important to identify how the microbiome interacts with hematopoietic stem cells (HSCs). The gut microbiota has been shown to influence the development and outcomes of hematologic disorders, suggesting dysbiosis may influence the maintenance of HSCs with age. Short chain fatty acids (SCFAs), lactate, iron availability, tryptophan metabolites, bacterial extracellular vesicles, microbe associated molecular patterns (MAMPs), and toll-like receptor (TLR) signalling have been proposed as key mediators of communication across the gut-bone marrow axis and will be reviewed in this article within the context of aging.
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Affiliation(s)
- Christopher Wells
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Tristan Robertson
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Prameet Sheth
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
- Division of Microbiology, Queen's University, Kingston, Ontario, Canada
- Department of Pathology and Molecular Medicine, Kingston, Ontario, Canada
| | - Sheela Abraham
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
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19
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Qin G, Dai J, Chien S, Martins TJ, Loera B, Nguyen QH, Oakes ML, Tercan B, Aguilar B, Hagen L, McCune J, Gelinas R, Monnat RJ, Shmulevich I, Becker PS. Mutation Patterns Predict Drug Sensitivity in Acute Myeloid Leukemia. Clin Cancer Res 2024; 30:2659-2671. [PMID: 38619278 PMCID: PMC11176916 DOI: 10.1158/1078-0432.ccr-23-1674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/15/2023] [Accepted: 12/08/2023] [Indexed: 04/16/2024]
Abstract
PURPOSE The inherent genetic heterogeneity of acute myeloid leukemia (AML) has challenged the development of precise and effective therapies. The objective of this study was to elucidate the genomic basis of drug resistance or sensitivity, identify signatures for drug response prediction, and provide resources to the research community. EXPERIMENTAL DESIGN We performed targeted sequencing, high-throughput drug screening, and single-cell genomic profiling on leukemia cell samples derived from patients with AML. Statistical approaches and machine learning models were applied to identify signatures for drug response prediction. We also integrated large public datasets to understand the co-occurring mutation patterns and further investigated the mutation profiles in the single cells. The features revealed in the co-occurring or mutual exclusivity pattern were further subjected to machine learning models. RESULTS We detected genetic signatures associated with sensitivity or resistance to specific agents, and identified five co-occurring mutation groups. The application of single-cell genomic sequencing unveiled the co-occurrence of variants at the individual cell level, highlighting the presence of distinct subclones within patients with AML. Using the mutation pattern for drug response prediction demonstrates high accuracy in predicting sensitivity to some drug classes, such as MEK inhibitors for RAS-mutated leukemia. CONCLUSIONS Our study highlights the importance of considering the gene mutation patterns for the prediction of drug response in AML. It provides a framework for categorizing patients with AML by mutations that enable drug sensitivity prediction.
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Affiliation(s)
| | - Jin Dai
- Division of Hematology, University of Washington, Seattle, Washington
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington
| | - Sylvia Chien
- Division of Hematology, University of Washington, Seattle, Washington
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington
| | - Timothy J. Martins
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington
| | - Brenda Loera
- City of Hope National Medical Center, Duarte, California
| | - Quy H. Nguyen
- University of California, Irvine, Irvine, California
| | | | - Bahar Tercan
- Institute for Systems Biology, Seattle, Washington
| | | | - Lauren Hagen
- Institute for Systems Biology, Seattle, Washington
| | | | | | - Raymond J. Monnat
- Lab Medicine|Pathology and Genome Sciences, University of Washington, Seattle, Washington
| | | | - Pamela S. Becker
- Division of Hematology, University of Washington, Seattle, Washington
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington
- City of Hope National Medical Center, Duarte, California
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20
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Álvarez N, Martín A, Dorado S, Colmenares R, Rufián L, Rodríguez M, Giménez A, Carneros L, Sanchez R, Carreño G, Rapado I, Heredia Y, Martínez-López J, Barrio S, Ayala R. Detection of minimal residual disease in acute myeloid leukemia: evaluating utility and challenges. Front Immunol 2024; 15:1252258. [PMID: 38938565 PMCID: PMC11210172 DOI: 10.3389/fimmu.2024.1252258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 04/29/2024] [Indexed: 06/29/2024] Open
Abstract
This study discusses the importance of minimal residual disease (MRD) detection in acute myeloid leukemia (AML) patients using liquid biopsy and next-generation sequencing (NGS). AML prognosis is based on various factors, including genetic alterations. NGS has revealed the molecular complexity of AML and helped refine risk stratification and personalized therapies. The long-term survival rates for AML patients are low, and MRD assessment is crucial in predicting prognosis. Currently, the most common methods for MRD detection are flow cytometry and quantitative PCR, but NGS is being incorporated into clinical practice due to its ability to detect genomic aberrations in the majority of AML patients. Typically, bone marrow samples are used for MRD assessment, but using peripheral blood samples or liquid biopsies would be less invasive. Leukemia originates in the bone marrow, along with the cfDNA obtained from peripheral blood. This study aimed to assess the utility of cell-free DNA (cfDNA) from peripheral blood samples for MRD detection in AML patients. A cohort of 20 AML patients was analyzed using NGS, and a correlation between MRD assessment by cfDNA and circulating tumor cells (CTCs) in paired samples was observed. Furthermore, a higher tumor signal was detected in cfDNA compared to CTCs, indicating greater sensitivity. Challenges for the application of liquid biopsy in MRD assessment were discussed, including the selection of appropriate markers and the sensitivity of certain markers. This study emphasizes the potential of liquid biopsy using cfDNA for MRD detection in AML patients and highlights the need for further research in this area.
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Affiliation(s)
- Noemí Álvarez
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, Madrid, Spain
- Hematological Malignancies Clinical Research Unit, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
| | - Alejandro Martín
- Hematological Malignancies Clinical Research Unit, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
- Altum Sequencing Co., Madrid, Spain
| | - Sara Dorado
- Altum Sequencing Co., Madrid, Spain
- Computational Science Department, Carlos III University, Madrid, Spain
| | - Rafael Colmenares
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, Madrid, Spain
| | - Laura Rufián
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, Madrid, Spain
- Altum Sequencing Co., Madrid, Spain
| | - Margarita Rodríguez
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, Madrid, Spain
- Altum Sequencing Co., Madrid, Spain
| | - Alicia Giménez
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, Madrid, Spain
| | - Laura Carneros
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, Madrid, Spain
| | - Ricardo Sanchez
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, Madrid, Spain
| | - Gonzalo Carreño
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, Madrid, Spain
| | - Inmaculada Rapado
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, Madrid, Spain
| | | | - Joaquín Martínez-López
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, Madrid, Spain
- Hematological Malignancies Clinical Research Unit, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
- Department of Medicine, Complutense University of Madrid, Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Carlos III, Madrid, Spain
| | - Santiago Barrio
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, Madrid, Spain
- Hematological Malignancies Clinical Research Unit, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
- Altum Sequencing Co., Madrid, Spain
| | - Rosa Ayala
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, Madrid, Spain
- Hematological Malignancies Clinical Research Unit, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
- Department of Medicine, Complutense University of Madrid, Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Carlos III, Madrid, Spain
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21
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Nwosu GO, Ross DM, Powell JA, Pitson SM. Venetoclax therapy and emerging resistance mechanisms in acute myeloid leukaemia. Cell Death Dis 2024; 15:413. [PMID: 38866760 PMCID: PMC11169396 DOI: 10.1038/s41419-024-06810-7] [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: 03/21/2024] [Revised: 06/05/2024] [Accepted: 06/05/2024] [Indexed: 06/14/2024]
Abstract
Acute myeloid leukaemia (AML) is a highly aggressive and devastating malignancy of the bone marrow and blood. For decades, intensive chemotherapy has been the frontline treatment for AML but has yielded only poor patient outcomes as exemplified by a 5-year survival rate of < 30%, even in younger adults. As knowledge of the molecular underpinnings of AML has advanced, so too has the development new strategies with potential to improve the treatment of AML patients. To date the most promising of these targeted agents is the BH3-mimetic venetoclax which in combination with standard of care therapies, has manageable non-haematological toxicity and exhibits impressive efficacy. However, approximately 30% of AML patients fail to respond to venetoclax-based regimens and almost all treatment responders eventually relapse. Here, we review the emerging mechanisms of intrinsic and acquired venetoclax resistance in AML and highlight recent efforts to identify novel strategies to overcome resistance to venetoclax.
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Affiliation(s)
- Gus O Nwosu
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
- Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - David M Ross
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
- Adelaide Medical School, Faculty of Health Sciences, University of Adelaide, Adelaide, SA, Australia
- Department of Haematology, Royal Adelaide Hospital, Central Adelaide Local Health Network, Adelaide, SA, Australia
- Department of Haematology, Flinders University and Medical Centre, Adelaide, SA, Australia
| | - Jason A Powell
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia.
- Adelaide Medical School, Faculty of Health Sciences, University of Adelaide, Adelaide, SA, Australia.
| | - Stuart M Pitson
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia.
- Adelaide Medical School, Faculty of Health Sciences, University of Adelaide, Adelaide, SA, Australia.
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia.
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22
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Sadigh S, Kim AS. Molecular Pathology of Myeloid Neoplasms: Molecular Pattern Recognition. Clin Lab Med 2024; 44:339-353. [PMID: 38821648 DOI: 10.1016/j.cll.2023.08.007] [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] [Indexed: 06/02/2024]
Abstract
Despite the apparent complexity of the molecular genetic underpinnings of myeloid neoplasms, most myeloid mutational profiles can be understood within a simple framework. Somatic mutations accumulate in hematopoietic stem cells with aging and toxic insults, termed clonal hematopoiesis. These "old stem cells" mutations, predominantly in the epigenetic and RNA spliceosome pathways, act as "founding" driver mutations leading to a clonal myeloid neoplasm when sufficient in number and clone size. Subsequent mutations can create the genetic flavor of the myeloid neoplasm ("backseat" drivers) due to their enrichment in certain entities or act as progression events ("aggressive" drivers) during clonal evolution.
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Affiliation(s)
- Sam Sadigh
- Department of Pathology, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA
| | - Annette S Kim
- Division of Diagnostic Genetics and Genomics, Department of Pathology, University of Michigan/Michigan Medicine, 2800 Plymouth Road, NCRC 36-1221-79, Ann Arbor, MI 48109, USA.
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23
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Uryu H, Saeki K, Haeno H, Kapadia CD, Furudate K, Nangalia J, Chapman MS, Zhao L, Hsu JI, Zhao C, Chen S, Tanaka T, Li Z, Yang H, DiNardo C, Daver N, Pemmaraju N, Jain N, Ravandi F, Zhang J, Song X, Thompson E, Tang H, Little L, Gumbs C, Orlowski RZ, Qazilbash M, Bhalla K, Colla S, Kantarjian H, Shamanna RK, Ramos CB, Nakada D, Futreal PA, Shpall E, Goodell M, Garcia-Manero G, Takahashi K. Clonal evolution of hematopoietic stem cells after cancer chemotherapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.23.595594. [PMID: 38826462 PMCID: PMC11142159 DOI: 10.1101/2024.05.23.595594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Normal hematopoietic stem and progenitor cells (HSPCs) inherently accumulate somatic mutations and lose clonal diversity with age, processes implicated in the development of myeloid malignancies 1 . The impact of exogenous stressors, such as cancer chemotherapies, on the genomic integrity and clonal dynamics of normal HSPCs is not well defined. We conducted whole-genome sequencing on 1,032 single-cell-derived HSPC colonies from 10 patients with multiple myeloma (MM), who had undergone various chemotherapy regimens. Our findings reveal that melphalan treatment distinctly increases mutational burden with a unique mutation signature, whereas other MM chemotherapies do not significantly affect the normal mutation rate of HSPCs. Among these therapy-induced mutations were several oncogenic drivers such as TET2 and PPM1D . Phylogenetic analysis showed a clonal architecture in post-treatment HSPCs characterized by extensive convergent evolution of mutations in genes such as TP53 and PPM1D . Consequently, the clonal diversity and structure of post-treatment HSPCs mirror those observed in normal elderly individuals, suggesting an accelerated clonal aging due to chemotherapy. Furthermore, analysis of matched therapy-related myeloid neoplasm (t-MN) samples, which occurred 1-8 years later, enabled us to trace the clonal origin of t-MNs to a single HSPC clone among a group of clones with competing malignant potential, indicating the critical role of secondary mutations in dictating clonal dominance and malignant transformation. Our findings suggest that cancer chemotherapy promotes an oligoclonal architecture with multiple HSPC clones possessing competing leukemic potentials, setting the stage for the selective emergence of a singular clone that evolves into t-MNs after acquiring secondary mutations. These results underscore the importance of further systematic research to elucidate the long-term hematological consequences of cancer chemotherapy.
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24
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Schiroli G, Kartha V, Duarte FM, Kristiansen TA, Mayerhofer C, Shrestha R, Earl A, Hu Y, Tay T, Rhee C, Buenrostro JD, Scadden DT. Cell of origin epigenetic priming determines susceptibility to Tet2 mutation. Nat Commun 2024; 15:4325. [PMID: 38773071 PMCID: PMC11109152 DOI: 10.1038/s41467-024-48508-6] [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: 06/17/2023] [Accepted: 04/30/2024] [Indexed: 05/23/2024] Open
Abstract
Hematopoietic stem cell (HSC) mutations can result in clonal hematopoiesis (CH) with heterogeneous clinical outcomes. Here, we investigate how the cell state preceding Tet2 mutation impacts the pre-malignant phenotype. Using an inducible system for clonal analysis of myeloid progenitors, we find that the epigenetic features of clones at similar differentiation status are highly heterogeneous and functionally respond differently to Tet2 mutation. Cell differentiation stage also influences Tet2 mutation response indicating that the cell of origin's epigenome modulates clone-specific behaviors in CH. Molecular features associated with higher risk outcomes include Sox4 that sensitizes cells to Tet2 inactivation, inducing dedifferentiation, altered metabolism and increasing the in vivo clonal output of mutant cells, as confirmed in primary GMP and HSC models. Our findings validate the hypothesis that epigenetic features can predispose specific clones for dominance, explaining why identical genetic mutations can result in different phenotypes.
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Affiliation(s)
- Giulia Schiroli
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
| | - Vinay Kartha
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Fabiana M Duarte
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Trine A Kristiansen
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
| | - Christina Mayerhofer
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
| | - Rojesh Shrestha
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Andrew Earl
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Yan Hu
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Tristan Tay
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Catherine Rhee
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
| | - Jason D Buenrostro
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA.
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA.
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | - David T Scadden
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA.
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA.
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25
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Lao Z, Ding LW, Sun QY, Jia L, Yan B, Ng AYJ, Capinpin SM, Wang R, Ying L, Chng WJ, Phillip Koeffler H, Koh WP, Yuan JM, Yang H, Goh YT, Grigoropoulos N. A Pre-Leukemic DNA Methylation Signature in Healthy Individuals at Higher Risk for Developing Myeloid Malignancy. Clin Cancer Res 2024; 30:2170-2180. [PMID: 38437679 PMCID: PMC11096012 DOI: 10.1158/1078-0432.ccr-22-3804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 10/23/2023] [Accepted: 02/29/2024] [Indexed: 03/06/2024]
Abstract
PURPOSE DNA methylation alterations are widespread in acute myelogenous leukemia (AML) and myelodysplastic syndrome (MDS), some of which appear to have evolved independently of somatic mutations in epigenetic regulators. Although the presence of somatic mutations in peripheral blood can predict the risk of development of AML and MDS, its accuracy remains unsatisfactory. EXPERIMENTAL DESIGN We performed global DNA methylation profiling in a case control study nested within the Singapore Chinese Health Study to evaluate whether DNA methylation alterations were associated with AML/MDS development. Targeted deep sequencing and methylated DNA immunoprecipitation sequencing (MeDIP-seq) were performed on peripheral blood collected a median of 9.9 years before diagnosis of AML or MDS, together with age-matched still-healthy individuals as controls. RESULTS Sixty-six individuals who developed AML or MDS displayed significant DNA methylation changes in the peripheral blood compared with 167 age- and gender-matched controls who did not develop AML/MDS during the follow-up period. Alterations in methylation in the differentially methylation regions were associated with increased odds of developing AML/MDS. CONCLUSIONS The epigenetic changes may be acquired independently and before somatic mutations that are relevant for AML/MDS development. The association between methylation changes and the risk of pre-AML/MDS in these individuals was considerably stronger than somatic mutations, suggesting that methylation changes could be used as biomarkers for pre-AML/MDS screening.
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Affiliation(s)
- Zhentang Lao
- Department of Haematology, Singapore General Hospital, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Ling-Wen Ding
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Department of Pathology, National University of Singapore; Nanomedicine Translational Research Programme, Yong Yoo Lin School of Medicine, National University of Singapore. Singapore
| | - Qiao-Yang Sun
- Department of Haematology, Singapore General Hospital, Singapore
- Department of Neurology, Singapore General Hospital, National Neuroscience Institute, Singapore
| | - Li Jia
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Benedict Yan
- Department of Laboratory Medicine, National University Hospital, Singapore
| | | | - Sharah Mae Capinpin
- Healthy Longitudinal Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, National University of Singapore, Singapore
| | - Renwei Wang
- Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Li Ying
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Wee Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- NUS Center for Cancer Research and Dept of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- National University Cancer Institute, National University Health System, Singapore
| | - H Phillip Koeffler
- National University Cancer Institute, National University Health System, Singapore
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Woon-Puay Koh
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jian-Min Yuan
- Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania. USA
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Department of Biomedical Informatics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yeow Tee Goh
- Department of Haematology, Singapore General Hospital, Singapore
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26
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de Camargo Magalhães ES, Hubner SE, Brown BD, Qiu Y, Kornblau SM. Proteomics for optimizing therapy in acute myeloid leukemia: venetoclax plus hypomethylating agents versus conventional chemotherapy. Leukemia 2024; 38:1046-1056. [PMID: 38531950 DOI: 10.1038/s41375-024-02208-8] [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: 11/18/2023] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/28/2024]
Abstract
The use of Hypomethylating agents combined with Venetoclax (VH) for the treatment of Acute Myeloid Leukemia (AML) has greatly improved outcomes in recent years. However not all patients benefit from the VH regimen and a way to rationally select between VH and Conventional Chemotherapy (CC) for individual AML patients is needed. Here, we developed a proteomic-based triaging strategy using Reverse-phase Protein Arrays (RPPA) to optimize therapy selection. We evaluated the expression of 411 proteins in 810 newly diagnosed adult AML patients, identifying 109 prognostic proteins, that divided into five patient expression profiles, which are useful for optimizing therapy selection. Furthermore, using machine learning algorithms, we determined a set of 14 proteins, among those 109, that were able to accurately recommend therapy, making it feasible for clinical application. Next, we identified a group of patients who did not benefit from either VH or CC and proposed target-based approaches to improve outcomes. Finally, we calculated that the clinical use of our proteomic strategy would have led to a change in therapy for 30% of patients, resulting in a 43% improvement in OS, resulting in around 2600 more cures from AML per year in the United States.
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Affiliation(s)
| | - Stefan Edward Hubner
- John Sealy School of Medicine, The University of Texas Medical Branch at Galveston, Galveston, TX, 77555, USA
| | - Brandon Douglas Brown
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030-4009, USA
| | - Yihua Qiu
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030-4009, USA
| | - Steven Mitchell Kornblau
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030-4009, USA.
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27
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Rückert T, Romagnani C. Extrinsic and intrinsic drivers of natural killer cell clonality. Immunol Rev 2024; 323:80-106. [PMID: 38506411 DOI: 10.1111/imr.13324] [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] [Indexed: 03/21/2024]
Abstract
Clonal expansion of antigen-specific lymphocytes is the fundamental mechanism enabling potent adaptive immune responses and the generation of immune memory. Accompanied by pronounced epigenetic remodeling, the massive proliferation of individual cells generates a critical mass of effectors for the control of acute infections, as well as a pool of memory cells protecting against future pathogen encounters. Classically associated with the adaptive immune system, recent work has demonstrated that innate immune memory to human cytomegalovirus (CMV) infection is stably maintained as large clonal expansions of natural killer (NK) cells, raising questions on the mechanisms for clonal selection and expansion in the absence of re-arranged antigen receptors. Here, we discuss clonal NK cell memory in the context of the mechanisms underlying clonal competition of adaptive lymphocytes and propose alternative selection mechanisms that might decide on the clonal success of their innate counterparts. We propose that the integration of external cues with cell-intrinsic sources of heterogeneity, such as variegated receptor expression, transcriptional states, and somatic variants, compose a bottleneck for clonal selection, contributing to the large size of memory NK cell clones.
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Affiliation(s)
- Timo Rückert
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Immunology, Berlin, Germany
| | - Chiara Romagnani
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Immunology, Berlin, Germany
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28
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McConville BM, Thomas T, Beckner R, Valadez C, Chook Y, Chung S, Liszczak G. Enigmatic missense mutations can cause disease via creation of de novo nuclear export signals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.24.590854. [PMID: 38712034 PMCID: PMC11071533 DOI: 10.1101/2024.04.24.590854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Disease-causing missense mutations that occur within structurally and functionally unannotated protein regions can guide researchers to new mechanisms of protein regulation and dysfunction. Here, we report that the thrombocytopenia-, myelodysplastic syndromes-, and leukemia-associated P214L mutation in the transcriptional regulator ETV6 creates an XPO1-dependent nuclear export signal to cause protein mislocalization. Strategies to disrupt XPO1 activity fully restore ETV6 P214L protein nuclear localization and transcription regulation activity. Mechanistic insight inspired the design of a 'humanized' ETV6 mice, which we employ to demonstrate that the germline P214L mutation is sufficient to elicit severe defects in thrombopoiesis and hematopoietic stem cell maintenance. Beyond ETV6, we employed computational methods to uncover rare disease-associated missense mutations in unrelated proteins that create a nuclear export signal to disrupt protein function. Thus, missense mutations that operate through this mechanism should be predictable and may suggest rational therapeutic strategies for associated diseases.
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29
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Kim D, Kim S, Song H, Gwak D, Min S, Byun JM, Koh Y, Hong J, Yoon S, Yun H, Shin D. Pursuing dynamics of minimal residual leukemic subclones in relapsed and refractory acute myeloid leukemia during conventional therapy. Cancer Med 2024; 13:e7182. [PMID: 38591109 PMCID: PMC11002636 DOI: 10.1002/cam4.7182] [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: 12/08/2023] [Revised: 02/23/2024] [Accepted: 03/29/2024] [Indexed: 04/10/2024] Open
Abstract
BACKGROUND Acute myeloid leukemia (AML) is characterized by clonal heterogeneity, leading to frequent relapses and drug resistance despite intensive clinical therapy. Although AML's clonal architecture has been addressed in many studies, practical monitoring of dynamic changes in those subclones during relapse and treatment is still understudied. METHOD Fifteen longitudinal bone marrow (BM) samples were collected from three relapsed and refractory (R/R) AML patients. Using droplet digital polymerase chain reaction (ddPCR), the frequencies of patient's leukemic variants were assessed in seven cell populations that were isolated from each BM sample based on cellular phenotypes. By quantifying mutant clones at the diagnosis, remission, and relapse stages, the distribution of AML subclones was sequentially monitored. RESULTS Minimal residual (MR) leukemic subclones exhibit heterogeneous distribution among BM cell populations, including mature leukocyte populations. During AML progression, these subclones undergo active phenotypic transitions and repopulate into distinct cell population regardless of normal hematopoiesis hierarchic order. Of these, MR subclones in progenitor populations of patient BM predominantly carry MR leukemic properties, leading to more robust expansion and stubborn persistence than those in mature populations. Moreover, a minor subset of MR leukemic subclones could be sustained at an extremely low frequency without clonal expansion during relapse. CONCLUSIONS In this study, we observed treatment persistent MR leukemic subclones and their phenotypic changes during the treatment process of R/R AML patients. This underscores the importance of preemptive inhibition of clonal promiscuity in R/R AML, proposing a practical method for monitoring AML MR subclones.
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Affiliation(s)
- Dongchan Kim
- Cancer Research InstituteSeoul National University College of MedicineSeoulRepublic of Korea
- Center for Medical InnovationSeoul National University HospitalSeoulRepublic of Korea
| | - Sheehyun Kim
- Center for Medical InnovationSeoul National University HospitalSeoulRepublic of Korea
- Center for Precision MedicineSeoul National University HospitalSeoulRepublic of Korea
| | - Hyojin Song
- Center for Medical InnovationSeoul National University HospitalSeoulRepublic of Korea
- Center for Precision MedicineSeoul National University HospitalSeoulRepublic of Korea
| | - Daehyeon Gwak
- Cancer Research InstituteSeoul National University College of MedicineSeoulRepublic of Korea
- Center for Medical InnovationSeoul National University HospitalSeoulRepublic of Korea
| | - Suji Min
- Cancer Research InstituteSeoul National University College of MedicineSeoulRepublic of Korea
- Center for Medical InnovationSeoul National University HospitalSeoulRepublic of Korea
| | - Ja Min Byun
- Cancer Research InstituteSeoul National University College of MedicineSeoulRepublic of Korea
- Center for Medical InnovationSeoul National University HospitalSeoulRepublic of Korea
- Department of Internal MedicineSeoul National University HospitalSeoulRepublic of Korea
| | - Youngil Koh
- Cancer Research InstituteSeoul National University College of MedicineSeoulRepublic of Korea
- Center for Medical InnovationSeoul National University HospitalSeoulRepublic of Korea
- Department of Internal MedicineSeoul National University HospitalSeoulRepublic of Korea
| | - Junshik Hong
- Cancer Research InstituteSeoul National University College of MedicineSeoulRepublic of Korea
- Center for Medical InnovationSeoul National University HospitalSeoulRepublic of Korea
- Department of Internal MedicineSeoul National University HospitalSeoulRepublic of Korea
| | - Sung‐Soo Yoon
- Cancer Research InstituteSeoul National University College of MedicineSeoulRepublic of Korea
- Center for Medical InnovationSeoul National University HospitalSeoulRepublic of Korea
- Department of Internal MedicineSeoul National University HospitalSeoulRepublic of Korea
| | - Hongseok Yun
- Center for Medical InnovationSeoul National University HospitalSeoulRepublic of Korea
- Center for Precision MedicineSeoul National University HospitalSeoulRepublic of Korea
| | - Dong‐Yeop Shin
- Cancer Research InstituteSeoul National University College of MedicineSeoulRepublic of Korea
- Center for Medical InnovationSeoul National University HospitalSeoulRepublic of Korea
- Department of Internal MedicineSeoul National University HospitalSeoulRepublic of Korea
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30
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Uechi L, Vasudevan S, Vilenski D, Branciamore S, Frankhouser D, O'Meally D, Meshinchi S, Marcucci G, Kuo YH, Rockne R, Kravchenko-Balasha N. Transcriptome free energy can serve as a dynamic patient-specific biomarker in acute myeloid leukemia. NPJ Syst Biol Appl 2024; 10:32. [PMID: 38527998 DOI: 10.1038/s41540-024-00352-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 02/26/2024] [Indexed: 03/27/2024] Open
Abstract
Acute myeloid leukemia (AML) is prevalent in both adult and pediatric patients. Despite advances in patient categorization, the heterogeneity of AML remains a challenge. Recent studies have explored the use of gene expression data to enhance AML diagnosis and prognosis, however, alternative approaches rooted in physics and chemistry may provide another level of insight into AML transformation. Utilizing publicly available databases, we analyze 884 human and mouse blood and bone marrow samples. We employ a personalized medicine strategy, combining state-transition theory and surprisal analysis, to assess the RNA transcriptome of individual patients. The transcriptome is transformed into physical parameters that represent each sample's steady state and the free energy change (FEC) from that steady state, which is the state with the lowest free energy.We found the transcriptome steady state was invariant across normal and AML samples. FEC, representing active molecular processes, varied significantly between samples and was used to create patient-specific barcodes to characterize the biology of the disease. We discovered that AML samples that were in a transition state had the highest FEC. This disease state may be characterized as the most unstable and hence the most therapeutically targetable since a change in free energy is a thermodynamic requirement for disease progression. We also found that distinct sets of ongoing processes may be at the root of otherwise similar clinical phenotypes, implying that our integrated analysis of transcriptome profiles may facilitate a personalized medicine approach to cure AML and restore a steady state in each patient.
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Affiliation(s)
- Lisa Uechi
- Division of Mathematical Oncology and Computational Systems Biology, Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Swetha Vasudevan
- The Institute of Biomedical and Oral Research, Faculty of Dental Medicine, The Hebrew University of Jerusalem, P.O.B. 12272, Ein Kerem, Jerusalem, 91120, Israel
| | - Daniela Vilenski
- The Institute of Biomedical and Oral Research, Faculty of Dental Medicine, The Hebrew University of Jerusalem, P.O.B. 12272, Ein Kerem, Jerusalem, 91120, Israel
| | - Sergio Branciamore
- Division of Mathematical Oncology and Computational Systems Biology, Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - David Frankhouser
- Division of Mathematical Oncology and Computational Systems Biology, Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Denis O'Meally
- Department of Diabetes and Cancer Discovery Science, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, D5-112, Seattle, WA, 98109, USA
| | - Guido Marcucci
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - Ya-Huei Kuo
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - Russell Rockne
- Division of Mathematical Oncology and Computational Systems Biology, Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA.
| | - Nataly Kravchenko-Balasha
- The Institute of Biomedical and Oral Research, Faculty of Dental Medicine, The Hebrew University of Jerusalem, P.O.B. 12272, Ein Kerem, Jerusalem, 91120, Israel.
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31
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Bandyopadhyay S, Duffy M, Ahn KJ, Pang M, Smith D, Duncan G, Sussman J, Zhang I, Huang J, Lin Y, Xiong B, Imtiaz T, Chen CH, Thadi A, Chen C, Xu J, Reichart M, Pillai V, Snaith O, Oldridge D, Bhattacharyya S, Maillard I, Carroll M, Nelson C, Qin L, Tan K. Mapping the Cellular Biogeography of Human Bone Marrow Niches Using Single-Cell Transcriptomics and Proteomic Imaging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.14.585083. [PMID: 38559168 PMCID: PMC10979999 DOI: 10.1101/2024.03.14.585083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The bone marrow is the organ responsible for blood production. Diverse non-hematopoietic cells contribute essentially to hematopoiesis. However, these cells and their spatial organization remain largely uncharacterized as they have been technically challenging to study in humans. Here, we used fresh femoral head samples and performed single-cell RNA sequencing (scRNA-Seq) to profile 29,325 enriched non-hematopoietic bone marrow cells and discover nine transcriptionally distinct subtypes. We next employed CO-detection by inDEXing (CODEX) multiplexed imaging of 18 individuals, including both healthy and acute myeloid leukemia (AML) samples, to spatially profile over one million single cells with a novel 53-antibody panel. We discovered a relatively hyperoxygenated arterio-endosteal niche for early myelopoiesis, and an adipocytic, but not endosteal or perivascular, niche for early hematopoietic stem and progenitor cells. We used our atlas to predict cell type labels in new bone marrow images and used these predictions to uncover mesenchymal stromal cell (MSC) expansion and leukemic blast/MSC-enriched spatial neighborhoods in AML patient samples. Our work represents the first comprehensive, spatially-resolved multiomic atlas of human bone marrow and will serve as a reference for future investigation of cellular interactions that drive hematopoiesis.
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Affiliation(s)
- Shovik Bandyopadhyay
- Cellular and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Medical Scientist Training Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Michael Duffy
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Kyung Jin Ahn
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Minxing Pang
- Applied Mathematics & Computational Science Graduate Group, University of Pennsylvania, Philadelphia, PA
| | - David Smith
- Center for Single Cell Biology, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Gwendolyn Duncan
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA
| | - Jonathan Sussman
- Medical Scientist Training Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Iris Zhang
- Department of Computer and Information Science, University of Pennsylvania, Philadelphia, PA
| | - Jeffrey Huang
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA
| | - Yulieh Lin
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Barbara Xiong
- Medical Scientist Training Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Tamjid Imtiaz
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA
| | - Chia-Hui Chen
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Anusha Thadi
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Changya Chen
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Jason Xu
- Medical Scientist Training Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Melissa Reichart
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Vinodh Pillai
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Oraine Snaith
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Derek Oldridge
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Siddharth Bhattacharyya
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Ivan Maillard
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Martin Carroll
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Charles Nelson
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Ling Qin
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Kai Tan
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
- Center for Single Cell Biology, Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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32
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Wu CH, Weng TF, Li JP, Wu KH. Biology and Therapeutic Properties of Mesenchymal Stem Cells in Leukemia. Int J Mol Sci 2024; 25:2527. [PMID: 38473775 DOI: 10.3390/ijms25052527] [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: 01/07/2024] [Revised: 02/08/2024] [Accepted: 02/15/2024] [Indexed: 03/14/2024] Open
Abstract
This comprehensive review delves into the multifaceted roles of mesenchymal stem cells (MSCs) in leukemia, focusing on their interactions within the bone marrow microenvironment and their impact on leukemia pathogenesis, progression, and treatment resistance. MSCs, characterized by their ability to differentiate into various cell types and modulate the immune system, are integral to the BM niche, influencing hematopoietic stem cell maintenance and functionality. This review extensively explores the intricate relationship between MSCs and leukemic cells in acute myeloid leukemia, acute lymphoblastic leukemia, chronic myeloid leukemia, and chronic lymphocytic leukemia. This review also addresses the potential clinical applications of MSCs in leukemia treatment. MSCs' role in hematopoietic stem cell transplantation, their antitumor effects, and strategies to disrupt chemo-resistance are discussed. Despite their therapeutic potential, the dual nature of MSCs in promoting and inhibiting tumor growth poses significant challenges. Further research is needed to understand MSCs' biological mechanisms in hematologic malignancies and develop targeted therapeutic strategies. This in-depth exploration of MSCs in leukemia provides crucial insights for advancing treatment modalities and improving patient outcomes in hematologic malignancies.
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Affiliation(s)
- Cheng-Hsien Wu
- School of Medicine, National Defense Medical Center, Taipei 114, Taiwan
| | - Te-Fu Weng
- Department of Pediatrics, Chung Shan Medical University Hospital, Taichung 402, Taiwan
- School of Medicine, Chung Shan Medical University, Taichung 402, Taiwan
| | - Ju-Pi Li
- Department of Pediatrics, Chung Shan Medical University Hospital, Taichung 402, Taiwan
- Department of Pathology, School of Medicine, Chung Shan Medical University, Taichung 402, Taiwan
| | - Kang-Hsi Wu
- Department of Pediatrics, Chung Shan Medical University Hospital, Taichung 402, Taiwan
- School of Medicine, Chung Shan Medical University, Taichung 402, Taiwan
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33
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Chea M, Rigolot L, Canali A, Vergez F. Minimal Residual Disease in Acute Myeloid Leukemia: Old and New Concepts. Int J Mol Sci 2024; 25:2150. [PMID: 38396825 PMCID: PMC10889505 DOI: 10.3390/ijms25042150] [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: 12/31/2023] [Revised: 02/01/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Minimal residual disease (MRD) is of major importance in onco-hematology, particularly in acute myeloid leukemia (AML). MRD measures the amount of leukemia cells remaining in a patient after treatment, and is an essential tool for disease monitoring, relapse prognosis, and guiding treatment decisions. Patients with a negative MRD tend to have superior disease-free and overall survival rates. Considerable effort has been made to standardize MRD practices. A variety of techniques, including flow cytometry and molecular methods, are used to assess MRD, each with distinct strengths and weaknesses. MRD is recognized not only as a predictive biomarker, but also as a prognostic tool and marker of treatment efficacy. Expected advances in MRD assessment encompass molecular techniques such as NGS and digital PCR, as well as optimization strategies such as unsupervised flow cytometry analysis and leukemic stem cell monitoring. At present, there is no perfect method for measuring MRD, and significant advances are expected in the future to fully integrate MRD assessment into the management of AML patients.
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Affiliation(s)
- Mathias Chea
- Laboratoire d’Hématologie Biologique, Institut Universitaire du Cancer de Toulouse Oncopole, Centre Hospitalier Universitaire de Toulouse, 31059 Toulouse, France; (M.C.); (L.R.); (A.C.)
| | - Lucie Rigolot
- Laboratoire d’Hématologie Biologique, Institut Universitaire du Cancer de Toulouse Oncopole, Centre Hospitalier Universitaire de Toulouse, 31059 Toulouse, France; (M.C.); (L.R.); (A.C.)
- School of Medicine, Université Toulouse III Paul Sabatier, 31062 Toulouse, France
| | - Alban Canali
- Laboratoire d’Hématologie Biologique, Institut Universitaire du Cancer de Toulouse Oncopole, Centre Hospitalier Universitaire de Toulouse, 31059 Toulouse, France; (M.C.); (L.R.); (A.C.)
- School of Medicine, Université Toulouse III Paul Sabatier, 31062 Toulouse, France
| | - Francois Vergez
- Laboratoire d’Hématologie Biologique, Institut Universitaire du Cancer de Toulouse Oncopole, Centre Hospitalier Universitaire de Toulouse, 31059 Toulouse, France; (M.C.); (L.R.); (A.C.)
- School of Medicine, Université Toulouse III Paul Sabatier, 31062 Toulouse, France
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34
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Stanger BZ, Wahl GM. Cancer as a Disease of Development Gone Awry. ANNUAL REVIEW OF PATHOLOGY 2024; 19:397-421. [PMID: 37832945 DOI: 10.1146/annurev-pathmechdis-031621-025610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
In the 160 years since Rudolf Virchow first postulated that neoplasia arises by the same law that regulates embryonic development, scientists have come to recognize the striking overlap between the molecular and cellular programs used by cancers and embryos. Advances in cancer biology and molecular techniques have further highlighted the similarities between carcinogenesis and embryogenesis, where cellular growth, differentiation, motility, and intercellular cross talk are mediated by common drivers and regulatory networks. This review highlights the many connections linking cancer biology and developmental biology to provide a deeper understanding of how a tissue's developmental history may both enable and constrain cancer cell evolution.
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Affiliation(s)
- Ben Z Stanger
- Division of Gastroenterology, Department of Medicine, Abramson Family Cancer Research Institute, and Department of Cell and Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA;
| | - Geoffrey M Wahl
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA;
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35
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O'Brien G, Cecotka A, Manola KN, Pagoni MN, Polanska J, Badie C. Epigenetic signature of ionizing radiation in therapy-related AML patients. Heliyon 2024; 10:e23244. [PMID: 38163095 PMCID: PMC10757008 DOI: 10.1016/j.heliyon.2023.e23244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/26/2023] [Accepted: 11/29/2023] [Indexed: 01/03/2024] Open
Abstract
Therapy-related acute myeloid leukaemia (t-AML) is a late side effect of previous chemotherapy (ct-AML) and/or radiotherapy (rt-AML) or immunosuppressive treatment. t-AMLs, which account for ∼10-20 % of all AML cases, are extremely aggressive and have a poor prognosis compared to de novo AML. Our hypothesis is that exposure to radiation causes genome-wide epigenetic changes in rt-AML. An epigenome-wide association study was undertaken, measuring over 850K methylation sites across the genome from fifteen donors (five healthy, five de novo, and five t-AMLs). The study predominantly focussed on 94K sites that lie in CpG-rich gene promoter regions. Genome-wide hypomethylation was discovered in AML, primarily in intergenic regions. Additionally, genes specific to AML were identified with promoter hypermethylation. A two-step validation was conducted, both internally, using pyrosequencing to measure methylation levels in specific regions across fifteen primary samples, and externally, with an additional eight AML samples. We demonstrated that the MEST and GATA5 gene promoters, which were previously identified as tumour suppressors, were noticeably hypermethylated in rt-AML, as opposed to other subtypes of AML and control samples. These may indicate the epigenetic involvement in the development of rt-AML at the molecular level and could serve as potential targets for drug therapy in rt-AML.
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Affiliation(s)
- Gráinne O'Brien
- Cancer Mechanisms and Biomarkers Group, Radiation Effects Department Radiation, Chemical & Environmental Hazards, Harwell Campus, Chilton, Didcot, Oxfordshire OX11 ORQ, UK Health Security Agency (UKHSA), United Kingdom
| | - Agnieszka Cecotka
- Department of Data Science and Engineering, Silesian University of Technology, 44-121 Gliwice, Poland
| | - Kalliopi N. Manola
- Department of Biodiagnostic Sciences and Technologies, INRASTES, National Centre for Research' Demokritos', 15341 Agia Paraskevi, Greece
| | - Maria N. Pagoni
- Hematology-Lymphomas Department - BMT Unit, Evangelismos Hospital, 10676 Athens, Greece
| | - Joanna Polanska
- Department of Data Science and Engineering, Silesian University of Technology, 44-121 Gliwice, Poland
| | - Christophe Badie
- Cancer Mechanisms and Biomarkers Group, Radiation Effects Department Radiation, Chemical & Environmental Hazards, Harwell Campus, Chilton, Didcot, Oxfordshire OX11 ORQ, UK Health Security Agency (UKHSA), United Kingdom
- Environmental Research Group Within the School of Public Health, Faculty of Medicine at Imperial College of Science, Technology and Medicine, London W12 0BZ, United Kingdom
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36
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Florio D, Marasco D. Could Targeting NPM1c+ Misfolding Be a Promising Strategy for Combating Acute Myeloid Leukemia? Int J Mol Sci 2024; 25:811. [PMID: 38255885 PMCID: PMC10815591 DOI: 10.3390/ijms25020811] [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: 12/03/2023] [Revised: 12/30/2023] [Accepted: 01/06/2024] [Indexed: 01/24/2024] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous group of diseases classified into various types on the basis of distinct features concerning the morphology, cytochemistry and cytogenesis of leukemic cells. Among the different subtypes, the group "AML with gene mutations" includes the variations of the gene of the multifunctional protein nucleophosmin 1 (NPM1). These mutations are the most frequent (~30-35% of AML adult patients and less in pediatric ones) and occur predominantly in the C-terminal domain (CTD) of NPM1. The most important mutation is the insertion at W288, which determines the frame shift W288Cfs12/Ffs12/Lfs*12 and leads to the addition of 2-12 amino acids, which hamper the correct folding of NPM1. This mutation leads to the loss of the nuclear localization signal (NoLS) and to aberrant cytoplasmic localization, denoted as NPM1c+. Many investigations demonstrated that interfering with the cellular location and oligomerization status of NPM1 can influence its biological functions, including the proper buildup of the nucleolus, and therapeutic strategies have been proposed to target NPM1c+, particularly the use of drugs able to re-direct NPM1 localization. Our studies unveiled a direct link between AML mutations and the neat amyloidogenic character of the CTDs of NPM1c+. Herein, with the aim of exploiting these conformational features, novel therapeutic strategies are proposed that rely on the induction of the selective self-cytotoxicity of leukemic blasts by focusing on agents such as peptides, peptoids or small molecules able to enhance amyloid aggregation and targeting selectively AML-NPM1c+ mutations.
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Affiliation(s)
| | - Daniela Marasco
- Department of Pharmacy, University of Naples “Federico II”, 80131 Naples, Italy;
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Liu M, Hong Y, Duan X, Zhou Q, Chen J, Liu S, Su J, Han L, Zhang J, Niu B. Unveiling the metal mutation nexus: Exploring the genomic impacts of heavy metal exposure in lung adenocarcinoma and colorectal cancer. JOURNAL OF HAZARDOUS MATERIALS 2024; 461:132590. [PMID: 37769449 DOI: 10.1016/j.jhazmat.2023.132590] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/06/2023] [Accepted: 09/19/2023] [Indexed: 09/30/2023]
Abstract
Mutations that activate oncogenes and deactivate tumor suppressor genes are widely recognized as significant contributors to cancer development. We investigated relationships between heavy metal exposure and the frequencies and types of gene mutations in patients with lung adenocarcinoma (LUAD) and colorectal cancer (CRC). Plasma concentrations of arsenic (As), cadmium (Cd), chromium (Cr), mercury (Hg), and lead (Pb) were measured using inductively coupled plasma mass spectrometry (ICPMS), and next-generation sequencing (NGS) of 1123 cancer-related genes was performed using the tumor tissues. Through Bayesian kernel machine regression (BKMR) analysis, we found associations between the integrated concentrations of the heavy metals and the number of gene mutations, especially insertions/deletions (indels), and Pb, As, and Cd were found to be the most significant contributors to the increased mutation rates. We extracted previously established mutational signatures and observed that they exhibit significant correlations with metal exposure. Moreover, we detected substantial shifts in the mutational landscape when comparing groups with high and low metal exposures. Several frequently mutated genes displayed positive correlations with metal exposure, whereas EGFR indels showed a negative association with Cd exposure. These findings suggest that heavy metal exposure can impact genomic stability in cancer-related genes, underscoring the importance of heavy metal exposure in cancer development.
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Affiliation(s)
- Mengyuan Liu
- Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China; WillingMed Technology (Beijing) Co., Ltd, Beijing 100176, China; Beijing ChosenMed Clinical Laboratory Co., Ltd., Beijing 100176, China
| | - Yuting Hong
- Department of Epidemiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Xiaohong Duan
- Beijing ChosenMed Clinical Laboratory Co., Ltd., Beijing 100176, China
| | - Qiming Zhou
- Beijing ChosenMed Clinical Laboratory Co., Ltd., Beijing 100176, China
| | - Jing Chen
- Beijing ChosenMed Clinical Laboratory Co., Ltd., Beijing 100176, China
| | - Siyao Liu
- Beijing ChosenMed Clinical Laboratory Co., Ltd., Beijing 100176, China
| | - Junyan Su
- Beijing ChosenMed Clinical Laboratory Co., Ltd., Beijing 100176, China
| | - Li Han
- Beijing ChosenMed Clinical Laboratory Co., Ltd., Beijing 100176, China
| | - Jiali Zhang
- Beijing ChosenMed Clinical Laboratory Co., Ltd., Beijing 100176, China
| | - Beifang Niu
- Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China; School of Computer Science, University of the Chinese Academy of Sciences, Beijing 100190, China.
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38
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Thol F, Döhner H, Ganser A. How I treat refractory and relapsed acute myeloid leukemia. Blood 2024; 143:11-20. [PMID: 37944143 DOI: 10.1182/blood.2023022481] [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: 09/12/2023] [Revised: 10/11/2023] [Accepted: 10/29/2023] [Indexed: 11/12/2023] Open
Abstract
ABSTRACT Most patients with acute myeloid leukemia (AML) develop refractory/relapsed (R/R) disease even in the presence of novel and targeted therapies. Given the biological complexity of the disease and differences in frontline treatments, there are therapies approved for only subgroups of R/R AML, and enrollment in clinical trials should be first priority. Allogeneic hematopoietic cell transplantation (HCT) is the only potentially curative strategy for most patients. Therapeutic approaches, including allogeneic HCT, triggered by the presence of measurable residual disease (MRD), have recently evolved to prevent overt hematologic relapse. Salvage therapy with chemotherapy or targeted therapy is frequently administered before HCT to reduce the leukemic burden. Gilteritinib is approved by the Food and Drug Administration and European Medicines Agency for patients with relapsed FLT3 mutated AML, whereas targeted therapy for relapsed IDH1/2 mutated AML has only FDA approval. Patients who are R/R after azacitidine and venetoclax (AZA/VEN) have a dismal outcome. In this setting, even available targeted therapies show unsatisfactory results. Examples of ongoing developments include menin inhibitors, a targeted therapy for patients with mutated NPM1 or KMT2A rearrangements, antibodies targeting the macrophage immune checkpoint CD47, and triple combinations involving AZA/VEN. The latter cause significant myelosuppressive effects, which make it challenging to find the right schedule and dose.
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Affiliation(s)
- Felicitas Thol
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Hartmut Döhner
- Department of Internal Medicine III, University of Ulm, Ulm, Germany
| | - Arnold Ganser
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
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Dong Q, Chen C, Hu Y, Zhang W, Yang X, Qi Y, Zhu C, Chen X, Shen X, Ji W. Clinical application of molecular residual disease detection by circulation tumor DNA in solid cancers and a comparison of technologies: review article. Cancer Biol Ther 2023; 24:2274123. [PMID: 37955635 PMCID: PMC10653633 DOI: 10.1080/15384047.2023.2274123] [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: 05/11/2023] [Accepted: 08/04/2023] [Indexed: 11/14/2023] Open
Abstract
Molecular residual disease (MRD), detected by circulating tumor DNA (ctDNA) can be involved in the entire process of solid tumor management, including recurrence prediction, efficacy evaluation, and risk stratification. Currently, the detection technologies are divided into two main categories, as follows: tumor-agnostic and tumor informed. Tumor-informed assay obtains mutation information by sequencing tumor tissue samples before blood MRD monitoring, followed by formulation of a personalized MRD panel. Tumor-agnostic assays are carried out using a fixed panel without the mutation information from primary tumor tissue. The choice of testing strategy may depend on the level of evidence from ongoing randomized clinical trials, investigator preference, cost-effectiveness, patient economics, and availability of tumor tissue. The review describes the difference between tumor informed and tumor agnostic detection. In addition, the clinical application of ctDNA MRD in solid tumors was introduced, with emphasis on lung cancer, colorectal cancer, Urinary system cancer, and breast cancer.
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Affiliation(s)
- Qiantong Dong
- Department of Gastrointestinal Surveillance, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Lucheng District, Wenzhou, Zhejiang, China
| | - Chenbin Chen
- Department of Gastrointestinal Surveillance, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Lucheng District, Wenzhou, Zhejiang, China
- Department of Gastrointestinal Surveillance, The First Affiliated Hospital of Wenzhou Medical University, Ouhai District, Wenzhou City, Zhejiang, China
| | - Yuanbo Hu
- Department of Gastrointestinal Surveillance, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Lucheng District, Wenzhou, Zhejiang, China
- Department of Gastrointestinal Surveillance, The First Affiliated Hospital of Wenzhou Medical University, Ouhai District, Wenzhou City, Zhejiang, China
| | - Weiteng Zhang
- Department of Gastrointestinal Surveillance, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Lucheng District, Wenzhou, Zhejiang, China
| | - Xinxin Yang
- Department of Gastrointestinal Surveillance, The First Affiliated Hospital of Wenzhou Medical University, Ouhai District, Wenzhou City, Zhejiang, China
| | - Yingxue Qi
- The Medical Department, Jiangsu Simcere Diagnostics Co.Ltd, The state Key Laboratory of Neurology and Oncology Drug Development, Nanjing, China
| | - Chan Zhu
- The Medical Department, Jiangsu Simcere Diagnostics Co.Ltd, The state Key Laboratory of Neurology and Oncology Drug Development, Nanjing, China
| | - Xiaodong Chen
- Department of Gastrointestinal Surveillance, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Lucheng District, Wenzhou, Zhejiang, China
| | - Xian Shen
- Department of Gastrointestinal Surveillance, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Lucheng District, Wenzhou, Zhejiang, China
- Department of Gastrointestinal Surveillance, The First Affiliated Hospital of Wenzhou Medical University, Ouhai District, Wenzhou City, Zhejiang, China
| | - Weiping Ji
- Department of Gastrointestinal Surveillance, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Lucheng District, Wenzhou, Zhejiang, China
- Department of Gastrointestinal Surveillance, The First Affiliated Hospital of Wenzhou Medical University, Ouhai District, Wenzhou City, Zhejiang, China
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40
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Weeks LD, Ebert BL. Causes and consequences of clonal hematopoiesis. Blood 2023; 142:2235-2246. [PMID: 37931207 PMCID: PMC10862247 DOI: 10.1182/blood.2023022222] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/25/2023] [Accepted: 10/25/2023] [Indexed: 11/08/2023] Open
Abstract
ABSTRACT Clonal hematopoiesis (CH) is described as the outsized contribution of expanded clones of hematopoietic stem and progenitor cells (HSPCs) to blood cell production. The prevalence of CH increases dramatically with age. CH can be caused by somatic mutations in individual genes or by gains and/or losses of larger chromosomal segments. CH is a premalignant state; the somatic mutations detected in CH are the initiating mutations for hematologic malignancies, and CH is a strong predictor of the development of blood cancers. Moreover, CH is associated with nonmalignant disorders and increased overall mortality. The somatic mutations that drive clonal expansion of HSPCs can alter the function of terminally differentiated blood cells, including the release of elevated levels of inflammatory cytokines. These cytokines may then contribute to a broad range of inflammatory disorders that increase in prevalence with age. Specific somatic mutations in the peripheral blood in coordination with blood count parameters can powerfully predict the development of hematologic malignancies and overall mortality in CH. In this review, we summarize the current understanding of CH nosology and origins. We provide an overview of available tools for risk stratification and discuss management strategies for patients with CH presenting to hematology clinics.
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Affiliation(s)
- Lachelle D. Weeks
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Center for Early Detection and Interception of Blood Cancers, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Benjamin L. Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Center for Early Detection and Interception of Blood Cancers, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- Howard Hughes Medical Institute, Boston, MA
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41
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García-Álvarez M, Yeguas A, Jiménez C, Medina-Herrera A, González-Calle V, Hernández-Ruano M, Maldonado R, Aires I, Casquero C, Sánchez-Villares I, Balanzategui A, Sarasquete ME, Alcoceba M, Vidriales MB, González-Díaz M, García-Sanz R, Chillón MC. Single-Cell DNA Sequencing and Immunophenotypic Profiling to Track Clonal Evolution in an Acute Myeloid Leukemia Patient. Biomedicines 2023; 12:66. [PMID: 38255173 PMCID: PMC10813288 DOI: 10.3390/biomedicines12010066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 01/24/2024] Open
Abstract
Single-cell DNA sequencing can address the sequence of somatic genetic events during myeloid transformation in relapsed acute myeloid leukemia (AML). We present an NPM1-mutated AML patient with an initial low ratio of FLT3-ITD (low-risk ELN-2017), treated with midostaurin combined with standard chemotherapy as front-line treatment, and with salvage therapy plus gilteritinib following allogenic stem cell transplantation after relapse. Simultaneous single-cell DNA sequencing and cell-surface immunophenotyping was used in diagnostic and relapse samples to understand the clinical scenario of this patient and to reconstruct the clonal composition of both tumors. Four independent clones were present before treatment: DNMT3A/DNMT3A/NPM1 (63.9%), DNMT3A/DNMT3A (13.9%), DNMT3A/DNMT3A/NPM1/FLT3 (13.8%), as well as a wild-type clone (8.3%), but only the minor clone with FLT3-ITD survived and expanded after therapy, being the most represented one (58.6%) at relapse. FLT3-ITD was subclonal and was found only in the myeloid blast population (CD38/CD117/CD123). Our study shows the usefulness of this approach to reveal the clonal architecture of the leukemia and the identification of small subclones at diagnosis and relapse that may explain how the neoplastic cells can escape from the activity of different treatments in a stepwise process that impedes the disease cure despite different stages of complete remission.
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Affiliation(s)
- María García-Álvarez
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), 37007 Salamanca, Spain; (M.G.-Á.); (C.J.); (A.M.-H.); (V.G.-C.); (M.H.-R.); (R.M.); (I.A.); (C.C.); (I.S.-V.); (A.B.); (M.E.S.); (M.A.); (M.B.V.); (M.G.-D.); (M.C.C.)
| | - Ana Yeguas
- Hematology Department, Complejo Asistencial Universitario de Palencia, 34005 Palencia, Spain;
| | - Cristina Jiménez
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), 37007 Salamanca, Spain; (M.G.-Á.); (C.J.); (A.M.-H.); (V.G.-C.); (M.H.-R.); (R.M.); (I.A.); (C.C.); (I.S.-V.); (A.B.); (M.E.S.); (M.A.); (M.B.V.); (M.G.-D.); (M.C.C.)
| | - Alejandro Medina-Herrera
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), 37007 Salamanca, Spain; (M.G.-Á.); (C.J.); (A.M.-H.); (V.G.-C.); (M.H.-R.); (R.M.); (I.A.); (C.C.); (I.S.-V.); (A.B.); (M.E.S.); (M.A.); (M.B.V.); (M.G.-D.); (M.C.C.)
| | - Verónica González-Calle
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), 37007 Salamanca, Spain; (M.G.-Á.); (C.J.); (A.M.-H.); (V.G.-C.); (M.H.-R.); (R.M.); (I.A.); (C.C.); (I.S.-V.); (A.B.); (M.E.S.); (M.A.); (M.B.V.); (M.G.-D.); (M.C.C.)
| | - Montserrat Hernández-Ruano
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), 37007 Salamanca, Spain; (M.G.-Á.); (C.J.); (A.M.-H.); (V.G.-C.); (M.H.-R.); (R.M.); (I.A.); (C.C.); (I.S.-V.); (A.B.); (M.E.S.); (M.A.); (M.B.V.); (M.G.-D.); (M.C.C.)
| | - Rebeca Maldonado
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), 37007 Salamanca, Spain; (M.G.-Á.); (C.J.); (A.M.-H.); (V.G.-C.); (M.H.-R.); (R.M.); (I.A.); (C.C.); (I.S.-V.); (A.B.); (M.E.S.); (M.A.); (M.B.V.); (M.G.-D.); (M.C.C.)
| | - Irene Aires
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), 37007 Salamanca, Spain; (M.G.-Á.); (C.J.); (A.M.-H.); (V.G.-C.); (M.H.-R.); (R.M.); (I.A.); (C.C.); (I.S.-V.); (A.B.); (M.E.S.); (M.A.); (M.B.V.); (M.G.-D.); (M.C.C.)
| | - Cristina Casquero
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), 37007 Salamanca, Spain; (M.G.-Á.); (C.J.); (A.M.-H.); (V.G.-C.); (M.H.-R.); (R.M.); (I.A.); (C.C.); (I.S.-V.); (A.B.); (M.E.S.); (M.A.); (M.B.V.); (M.G.-D.); (M.C.C.)
| | - Inmaculada Sánchez-Villares
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), 37007 Salamanca, Spain; (M.G.-Á.); (C.J.); (A.M.-H.); (V.G.-C.); (M.H.-R.); (R.M.); (I.A.); (C.C.); (I.S.-V.); (A.B.); (M.E.S.); (M.A.); (M.B.V.); (M.G.-D.); (M.C.C.)
| | - Ana Balanzategui
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), 37007 Salamanca, Spain; (M.G.-Á.); (C.J.); (A.M.-H.); (V.G.-C.); (M.H.-R.); (R.M.); (I.A.); (C.C.); (I.S.-V.); (A.B.); (M.E.S.); (M.A.); (M.B.V.); (M.G.-D.); (M.C.C.)
| | - María Eugenia Sarasquete
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), 37007 Salamanca, Spain; (M.G.-Á.); (C.J.); (A.M.-H.); (V.G.-C.); (M.H.-R.); (R.M.); (I.A.); (C.C.); (I.S.-V.); (A.B.); (M.E.S.); (M.A.); (M.B.V.); (M.G.-D.); (M.C.C.)
| | - Miguel Alcoceba
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), 37007 Salamanca, Spain; (M.G.-Á.); (C.J.); (A.M.-H.); (V.G.-C.); (M.H.-R.); (R.M.); (I.A.); (C.C.); (I.S.-V.); (A.B.); (M.E.S.); (M.A.); (M.B.V.); (M.G.-D.); (M.C.C.)
| | - María Belén Vidriales
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), 37007 Salamanca, Spain; (M.G.-Á.); (C.J.); (A.M.-H.); (V.G.-C.); (M.H.-R.); (R.M.); (I.A.); (C.C.); (I.S.-V.); (A.B.); (M.E.S.); (M.A.); (M.B.V.); (M.G.-D.); (M.C.C.)
| | - Marcos González-Díaz
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), 37007 Salamanca, Spain; (M.G.-Á.); (C.J.); (A.M.-H.); (V.G.-C.); (M.H.-R.); (R.M.); (I.A.); (C.C.); (I.S.-V.); (A.B.); (M.E.S.); (M.A.); (M.B.V.); (M.G.-D.); (M.C.C.)
| | - Ramón García-Sanz
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), 37007 Salamanca, Spain; (M.G.-Á.); (C.J.); (A.M.-H.); (V.G.-C.); (M.H.-R.); (R.M.); (I.A.); (C.C.); (I.S.-V.); (A.B.); (M.E.S.); (M.A.); (M.B.V.); (M.G.-D.); (M.C.C.)
| | - María Carmen Chillón
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), 37007 Salamanca, Spain; (M.G.-Á.); (C.J.); (A.M.-H.); (V.G.-C.); (M.H.-R.); (R.M.); (I.A.); (C.C.); (I.S.-V.); (A.B.); (M.E.S.); (M.A.); (M.B.V.); (M.G.-D.); (M.C.C.)
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42
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Wang D, Rausch C, Buerger SA, Tschuri S, Rothenberg-Thurley M, Schulz M, Hasenauer J, Ziemann F, Metzeler KH, Marr C. Modeling early treatment response in AML from cell-free tumor DNA. iScience 2023; 26:108271. [PMID: 38047080 PMCID: PMC10690559 DOI: 10.1016/j.isci.2023.108271] [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: 06/16/2023] [Revised: 10/03/2023] [Accepted: 10/17/2023] [Indexed: 12/05/2023] Open
Abstract
Monitoring disease response after intensive chemotherapy for acute myeloid leukemia (AML) currently requires invasive bone marrow biopsies, imposing a significant burden on patients. In contrast, cell-free tumor DNA (ctDNA) in peripheral blood, carrying tumor-specific mutations, offers a less-invasive assessment of residual disease. However, the relationship between ctDNA levels and bone marrow blast kinetics remains unclear. We explored this in 10 AML patients with NPM1 and IDH2 mutations undergoing initial chemotherapy. Comparison of mathematical mixed-effect models showed that (1) inclusion of blast cell death in the bone marrow, (2) transition of ctDNA to peripheral blood, and (3) ctDNA decay in peripheral blood describes kinetics of blast cells and ctDNA best. The fitted model allows prediction of residual bone marrow blast content from ctDNA, and its scaling factor, representing clonal heterogeneity, correlates with relapse risk. Our study provides precise insights into blast and ctDNA kinetics, offering novel avenues for AML disease monitoring.
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Affiliation(s)
- Dantong Wang
- Institute of AI for Health, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg 85764, Germany
- Center for Mathematics, Technische Universität München, Garching 85748, Germany
| | - Christian Rausch
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital (LMU), Munich, Germany
- German Cancer Consortium (DKTK), partner sites Munich/Dresden, Germany
| | - Simon A. Buerger
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital (LMU), Munich, Germany
| | - Sebastian Tschuri
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital (LMU), Munich, Germany
| | - Maja Rothenberg-Thurley
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital (LMU), Munich, Germany
| | - Melanie Schulz
- Institute of AI for Health, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg 85764, Germany
- Center for Mathematics, Technische Universität München, Garching 85748, Germany
| | - Jan Hasenauer
- Center for Mathematics, Technische Universität München, Garching 85748, Germany
- Computational Health Center, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg 85764, Germany
- Faculty of Mathematics and Natural Sciences, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany
| | - Frank Ziemann
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital (LMU), Munich, Germany
- German Cancer Consortium (DKTK), partner sites Munich/Dresden, Germany
| | - Klaus H. Metzeler
- Department of Hematology and Cell Therapy, University Hospital Leipzig (UHL) 04103, Germany
| | - Carsten Marr
- Institute of AI for Health, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg 85764, Germany
- Center for Mathematics, Technische Universität München, Garching 85748, Germany
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Cacic AM, Schulz FI, Germing U, Dietrich S, Gattermann N. Molecular and clinical aspects relevant for counseling individuals with clonal hematopoiesis of indeterminate potential. Front Oncol 2023; 13:1303785. [PMID: 38162500 PMCID: PMC10754976 DOI: 10.3389/fonc.2023.1303785] [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: 09/28/2023] [Accepted: 11/28/2023] [Indexed: 01/03/2024] Open
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP) has fascinated the medical community for some time. Discovered about a decade ago, this phenomenon links age-related alterations in hematopoiesis not only to the later development of hematological malignancies but also to an increased risk of early-onset cardiovascular disease and some other disorders. CHIP is detected in the blood and is characterized by clonally expanded somatic mutations in cancer-associated genes, predisposing to the development of hematologic neoplasms such as MDS and AML. CHIP-associated mutations often involve DNA damage repair genes and are frequently observed following prior cytotoxic cancer therapy. Genetic predisposition seems to be a contributing factor. It came as a surprise that CHIP significantly elevates the risk of myocardial infarction and stroke, and also contributes to heart failure and pulmonary hypertension. Meanwhile, evidence of mutant clonal macrophages in vessel walls and organ parenchyma helps to explain the pathophysiology. Besides aging, there are some risk factors promoting the appearance of CHIP, such as smoking, chronic inflammation, chronic sleep deprivation, and high birth weight. This article describes fundamental aspects of CHIP and explains its association with hematologic malignancies, cardiovascular disorders, and other medical conditions, while also exploring potential progress in the clinical management of affected individuals. While it is important to diagnose conditions that can lead to adverse, but potentially preventable, effects, it is equally important not to stress patients by confronting them with disconcerting findings that cannot be remedied. Individuals with diagnosed or suspected CHIP should receive counseling in a specialized outpatient clinic, where professionals from relevant medical specialties may help them to avoid the development of CHIP-related health problems. Unfortunately, useful treatments and clinical guidelines for managing CHIP are still largely lacking. However, there are some promising approaches regarding the management of cardiovascular disease risk. In the future, strategies aimed at restoration of gene function or inhibition of inflammatory mediators may become an option.
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Affiliation(s)
- Anna Maria Cacic
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine Universität Düsseldorf, Düsseldorf, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Düsseldorf, Germany
| | - Felicitas Isabel Schulz
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine Universität Düsseldorf, Düsseldorf, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Düsseldorf, Germany
| | - Ulrich Germing
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine Universität Düsseldorf, Düsseldorf, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Düsseldorf, Germany
| | - Sascha Dietrich
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine Universität Düsseldorf, Düsseldorf, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Düsseldorf, Germany
| | - Norbert Gattermann
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine Universität Düsseldorf, Düsseldorf, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Düsseldorf, Germany
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Wang L, Qiu F, Shen Y, Chen S, Si P. Co-existence of KMT2A:: SEPTIN6 fusion and DIS3 variant in a pediatric case with acute myeloid leukemia: a case report and literature review. Front Oncol 2023; 13:1308786. [PMID: 38152368 PMCID: PMC10751303 DOI: 10.3389/fonc.2023.1308786] [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: 10/07/2023] [Accepted: 11/29/2023] [Indexed: 12/29/2023] Open
Abstract
The lysine(K)-specific methyltransferase 2A gene (KMT2A), previously known as mixed lineage leukemia (MLL), frequently rearranged in acute leukemia, belongs to one of the most promiscuous genes and has been found fused to more than 80 different partners. KMT2A::SEPTIN6 fusion is a relatively uncommon rearrangement observed in pediatric acute myeloid leukemia (AML) patients, some of which may harbor other mutations. We herein report a case of AML-M4-infant with KMT2A::SEPTIN6 fusion and DIS3 variant. The 8-month-old girl presented with leukocytosis, anemia and thrombocytopenia. A bone marrow smear disclosed that 64% of the total nucleated cells were blasts. Karyotype analysis showed 46,X,t(X;11)(q24;q23)[10]/46,XX[10]. Fluorescence in situ hybridization analysis suggested a possible break in the KMT2A gene. After whole transcriptome sequencing, Exon 9 of KMT2A was fused in-frame with Exon 2 of SEPTIN6. This is a typical type of chromosomal rearrangement leading to the KMT2A::SEPTIN6 fusion. Meanwhile, DIS3 variant [c.2065C>T, p.R689X, variant allele frequency (VAF): 39.8%] was identified. KMT2A::SEPTIN6 fusion has been associated with the pathogenesis of AML, whereas DIS3 variants are relatively rare genetic events in pediatric AML. Regrettably, the relatives disagreed with the combination chemotherapy, and the patient eventually died of progressive disease. In conclusion, our findings provide a foundation for a better understanding of the genotypic profile of KMT2A::SEPTIN6 associated AML, and the co-existence of KMT2A::SEPTIN6 and DIS3 variant might contribute to the disease progression and transformation of AML.
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Affiliation(s)
- Liang Wang
- Department of Clinical Laboratory, Tianjin Children’s Hospital/Children’s Hospital, Tianjin University, Tianjin, China
| | - Fangzhou Qiu
- Department of Clinical Laboratory, Tianjin Children’s Hospital/Children’s Hospital, Tianjin University, Tianjin, China
| | - Yongming Shen
- Department of Clinical Laboratory, Tianjin Children’s Hospital/Children’s Hospital, Tianjin University, Tianjin, China
| | - Sen Chen
- Department of Hematology, Tianjin Children’s Hospital/Children’s Hospital, Tianjin University, Tianjin, China
| | - Ping Si
- Department of Clinical Laboratory, Tianjin Children’s Hospital/Children’s Hospital, Tianjin University, Tianjin, China
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Yun JK, Kim S, An H, Lee GD, Kim HR, Kim YH, Kim DK, Park SI, Choi S, Koh Y. Pre-operative clonal hematopoiesis is related to adverse outcome in lung cancer after adjuvant therapy. Genome Med 2023; 15:111. [PMID: 38087308 PMCID: PMC10714617 DOI: 10.1186/s13073-023-01266-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Clonal hematopoiesis (CH) frequently progresses after chemotherapy or radiotherapy. We evaluated the clinical impact of preoperative CH on the survival outcomes of patients with non-small cell lung cancer (NSCLC) who underwent surgical resection followed by adjuvant therapy. METHODS A total of 415 consecutive patients with NSCLC who underwent surgery followed by adjuvant therapy from 2011 to 2017 were analyzed. CH status was evaluated using targeted deep sequencing of blood samples collected before surgery. To minimize the possible selection bias between the two groups according to CH status, a propensity score matching (PSM) was adopted. Early-stage patients were further analyzed with additional matched cohort of patients who did not receive adjuvant therapy. RESULTS CH was detected in 21% (86/415) of patients with NSCLC before adjuvant therapy. Patients with CH mutations had worse overall survival (OS) than those without (hazard ratio [95% confidence interval] = 1.56 [1.07-2.28], p = 0.020), which remained significant after the multivariable analysis (1.58 [1.08-2.32], p = 0.019). Of note, the presence of CH was associated with non-cancer mortality (p = 0.042) and mortality of unknown origin (p = 0.018). In patients with stage IIB NSCLC, there was a significant interaction on OS between CH and adjuvant therapy after the adjustment with several cofactors through the multivariable analysis (HR 1.19, 95% CI 1.00-1.1.41, p = 0.041). CONCLUSIONS In resected NSCLC, existence of preoperative CH might amplify CH-related adverse outcomes through adjuvant treatments, resulting in poor survival results.
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Affiliation(s)
- Jae Kwang Yun
- Department of Thoracic and Cardiovascular Surgery, Asan Medical Center, Ulsan University College of Medicine, 88, Olympic-Ro 43-Gil, Songpa-Gu, Seoul, Republic of Korea
| | - Sugyeong Kim
- Genome Opinion Inc., Sungsu SKV1 Center, 1-721, 48, Achasan-Ro 17-Gil, Seongdong-Gu, Seoul, Republic of Korea
| | - Hongyul An
- Genome Opinion Inc., Sungsu SKV1 Center, 1-721, 48, Achasan-Ro 17-Gil, Seongdong-Gu, Seoul, Republic of Korea
| | - Geun Dong Lee
- Department of Thoracic and Cardiovascular Surgery, Asan Medical Center, Ulsan University College of Medicine, 88, Olympic-Ro 43-Gil, Songpa-Gu, Seoul, Republic of Korea
| | - Hyeong Ryul Kim
- Department of Thoracic and Cardiovascular Surgery, Asan Medical Center, Ulsan University College of Medicine, 88, Olympic-Ro 43-Gil, Songpa-Gu, Seoul, Republic of Korea
| | - Yong-Hee Kim
- Department of Thoracic and Cardiovascular Surgery, Asan Medical Center, Ulsan University College of Medicine, 88, Olympic-Ro 43-Gil, Songpa-Gu, Seoul, Republic of Korea
| | - Dong Kwan Kim
- Department of Thoracic and Cardiovascular Surgery, Asan Medical Center, Ulsan University College of Medicine, 88, Olympic-Ro 43-Gil, Songpa-Gu, Seoul, Republic of Korea
| | - Seung-Il Park
- Department of Thoracic and Cardiovascular Surgery, Asan Medical Center, Ulsan University College of Medicine, 88, Olympic-Ro 43-Gil, Songpa-Gu, Seoul, Republic of Korea
| | - Sehoon Choi
- Department of Thoracic and Cardiovascular Surgery, Asan Medical Center, Ulsan University College of Medicine, 88, Olympic-Ro 43-Gil, Songpa-Gu, Seoul, Republic of Korea.
| | - Youngil Koh
- Genome Opinion Inc., Sungsu SKV1 Center, 1-721, 48, Achasan-Ro 17-Gil, Seongdong-Gu, Seoul, Republic of Korea.
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul National University Hospital, 101, Daehak-Ro, Jongno-Gu, Seoul, Republic of Korea.
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46
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Karpova D. Clonal hematopoiesis in frequent whole blood donors. HEMATOLOGY. AMERICAN SOCIETY OF HEMATOLOGY. EDUCATION PROGRAM 2023; 2023:299-304. [PMID: 38066913 PMCID: PMC10727091 DOI: 10.1182/hematology.2023000483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Healthy volunteer donors are committed to contributing key medical resources. Repeated, regular donation of whole blood represents a specific trigger of hematopoietic stress. Hematopoietic stem cells (HSCs) are known to respond to environmental triggers by altering their differentiation and/or proliferative behavior. This can manifest in long-term changes in the clonal dynamics of HSCs, such as the age-associated expansion of HSCs carrying somatic mutations in genes associated with hematologic cancers-that is, clonal hematopoiesis (CH). A recent study revealed a higher prevalence of CH in frequent donors driven by low-risk mutations in genes encoding for epigenetic modifiers, with DNMT3A and TET2 being the most common. No difference in the prevalence of known preleukemic driver mutations was detected between the cohorts, underscoring the safety of repetitive blood donations. Functional analyses suggest a link between the presence of selected DNMT3A mutations found in the frequent donor group and the responsiveness of the cells to the molecular mediator of bleeding stress, erythropoietin (EPO), but not inflammation. These findings define EPO as one of the environmental factors that provide a fitness advantage to specific mutant HSCs. Analyzing CH prevalence and characteristics in other donor cohorts will be important to comprehensively assess the health risks associated with the different types of donation.
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Affiliation(s)
- Darja Karpova
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO
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Spencer Chapman M, Cull AH, Ciuculescu MF, Esrick EB, Mitchell E, Jung H, O'Neill L, Roberts K, Fabre MA, Williams N, Nangalia J, Quinton J, Fox JM, Pellin D, Makani J, Armant M, Williams DA, Campbell PJ, Kent DG. Clonal selection of hematopoietic stem cells after gene therapy for sickle cell disease. Nat Med 2023; 29:3175-3183. [PMID: 37973947 PMCID: PMC10719109 DOI: 10.1038/s41591-023-02636-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 10/10/2023] [Indexed: 11/19/2023]
Abstract
Gene therapy (GT) provides a potentially curative treatment option for patients with sickle cell disease (SCD); however, the occurrence of myeloid malignancies in GT clinical trials has prompted concern, with several postulated mechanisms. Here, we used whole-genome sequencing to track hematopoietic stem cells (HSCs) from six patients with SCD at pre- and post-GT time points to map the somatic mutation and clonal landscape of gene-modified and unmodified HSCs. Pre-GT, phylogenetic trees were highly polyclonal and mutation burdens per cell were elevated in some, but not all, patients. Post-GT, no clonal expansions were identified among gene-modified or unmodified cells; however, an increased frequency of potential driver mutations associated with myeloid neoplasms or clonal hematopoiesis (DNMT3A- and EZH2-mutated clones in particular) was observed in both genetically modified and unmodified cells, suggesting positive selection of mutant clones during GT. This work sheds light on HSC clonal dynamics and the mutational landscape after GT in SCD, highlighting the enhanced fitness of some HSCs harboring pre-existing driver mutations. Future studies should define the long-term fate of mutant clones, including any contribution to expansions associated with myeloid neoplasms.
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Affiliation(s)
- Michael Spencer Chapman
- Wellcome Sanger Institute, Hinxton, UK
- Department of Haematology, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London, UK
- Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Alyssa H Cull
- York Biomedical Research Institute, University of York, York, UK
| | | | - Erica B Esrick
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Emily Mitchell
- Wellcome Sanger Institute, Hinxton, UK
- Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK
| | | | | | | | - Margarete A Fabre
- Wellcome Sanger Institute, Hinxton, UK
- Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | | | - Jyoti Nangalia
- Wellcome Sanger Institute, Hinxton, UK
- Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK
| | - Joanne Quinton
- York Biomedical Research Institute, University of York, York, UK
| | - James M Fox
- York Biomedical Research Institute, University of York, York, UK
| | - Danilo Pellin
- Harvard Medical School, Boston, MA, USA
- Gene Therapy Program, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA, USA
| | - Julie Makani
- Muhimbili University of Health and Allied Sciences (MUHAS), Dar-es-Salaam, Tanzania
- SickleInAfrica Clinical Coordinating Center, MUHAS, Dar-es-Salaam, Tanzania
- Imperial College London, London, UK
| | - Myriam Armant
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - David A Williams
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Gene Therapy Program, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
| | - Peter J Campbell
- Wellcome Sanger Institute, Hinxton, UK.
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK.
| | - David G Kent
- York Biomedical Research Institute, University of York, York, UK.
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48
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Hallermayr A, Keßler T, Steinke-Lange V, Heitzer E, Holinski-Feder E, Speicher M. The utility of liquid biopsy in clinical genetic diagnosis of cancer and monogenic mosaic disorders. MED GENET-BERLIN 2023; 35:275-284. [PMID: 38835734 PMCID: PMC11006364 DOI: 10.1515/medgen-2023-2066] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Liquid biopsy for minimally invasive diagnosis and monitoring of cancer patients is progressing toward routine clinical practice. With the implementation of highly sensitive next-generation sequencing (NGS) based assays for the analysis of cfDNA, however, consideration of the utility of liquid biopsy for clinical genetic testing is critical. While the focus of liquid biopsy for cancer diagnosis is the detection of circulating tumor DNA (ctDNA) as a fraction of total cell-free DNA (cfDNA), cfDNA analysis reveals both somatic mosaic tumor and germline variants and clonal hematopoiesis. Here we outline advantages and limitations of mosaic and germline variant detection as well as the impact of clonal hematopoiesis on liquid biopsy in cancer diagnosis. We also evaluate the potential of cfDNA analysis for the molecular diagnosis of monogenic mosaic disorders.
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Affiliation(s)
| | - Thomas Keßler
- MGZ - Medizinisch Genetisches Zentrum München Germany
| | | | - Ellen Heitzer
- Medical University of Graz Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine (Austria) Graz Austria
| | | | - Michael Speicher
- Medical University of Graz Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine (Austria), Neue Stiftingtalstraße 2 Graz Austria
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49
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Cui Z, Wei H, Goding C, Cui R. Stem cell heterogeneity, plasticity, and regulation. Life Sci 2023; 334:122240. [PMID: 37925141 DOI: 10.1016/j.lfs.2023.122240] [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: 09/08/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/06/2023]
Abstract
As a population of homogeneous cells with both self-renewal and differentiation potential, stem cell pools are highly compartmentalized and contain distinct subsets that exhibit stable but limited heterogeneity during homeostasis. However, their striking plasticity is showcased under natural or artificial stress, such as injury, transplantation, cancer, and aging, leading to changes in their phenotype, constitution, metabolism, and function. The complex and diverse network of cell-extrinsic niches and signaling pathways, together with cell-intrinsic genetic and epigenetic regulators, tightly regulate both the heterogeneity during homeostasis and the plasticity under perturbation. Manipulating these factors offers better control of stem cell behavior and a potential revolution in the current state of regenerative medicine. However, disruptions of normal regulation by genetic mutation or excessive plasticity acquisition may contribute to the formation of tumors. By harnessing innovative techniques that enhance our understanding of stem cell heterogeneity and employing novel approaches to maximize the utilization of stem cell plasticity, stem cell therapy holds immense promise for revolutionizing the future of medicine.
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Affiliation(s)
- Ziyang Cui
- Department of Dermatology and Venerology, Peking University First Hospital, Beijing 100034, China.
| | - Hope Wei
- Department of Biology, Boston University, 5 Cummington Mall, Boston, MA 02215, United States of America
| | - Colin Goding
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX37DQ, UK
| | - Rutao Cui
- Skin Disease Research Institute, The 2nd Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
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50
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Beeler JS, Bolton KL. How low can you go?: Methodologic considerations in clonal hematopoiesis variant calling. Leuk Res 2023; 135:107419. [PMID: 37956474 DOI: 10.1016/j.leukres.2023.107419] [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: 06/26/2023] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023]
Abstract
Clonal hematopoiesis (CH) is defined by the presence of an expanded clonal hematopoietic cell population due to an acquired mutation conferring a selective growth advantage and is known to predispose to hematologic malignancy. In this review, we discuss sequencing methods for CH detection in bulk sequencing data and corresponding bioinformatic approaches for variant calling, filtering, and curation. We detail practical recommendations for CH calling. Finally, we discuss how improvements in CH sequencing and bioinformatic approaches will enable the characterization of CH trajectories, its impact on human health, and therapeutic approaches to mitigate its adverse effects.
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Affiliation(s)
- J Scott Beeler
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Kelly L Bolton
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
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