1
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Li H, Chen Y, Ding M, Liu J, Sun H, Fang H, Brady SW, Xu Y, Glaser F, Ma X, Tang Y, Du L, Wu X, Wang S, Zhu L, Li B, Shen S, Zhang J, Zheng L, Yu J, Assaraf YG, Zhou BBS. Folylpolyglutamate synthetase inactivation in relapsed ALL induces a druggable folate metabolic vulnerability. Drug Resist Updat 2024; 77:101141. [PMID: 39181011 DOI: 10.1016/j.drup.2024.101141] [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: 03/05/2024] [Revised: 07/22/2024] [Accepted: 08/14/2024] [Indexed: 08/27/2024]
Abstract
AIMS The antifolate methotrexate (MTX) is an anchor drug used in acute lymphoblastic leukemia (ALL) with poorly understood chemoresistance mechanisms in relapse. Herein we find decreased folate polyglutamylation network activities and inactivating FPGS mutations, both of which could induce MTX resistance and folate metabolic vulnerability in relapsed ALL. METHODS We utilized integrated systems biology analysis of transcriptomic and genomic data from relapse ALL cohorts to infer hidden ALL relapse drivers and related genetic alternations during clonal evolution. The drug sensitivity assay was used to determine the impact of relapse-specific FPGS mutations on sensitivity to different antifolates and chemotherapeutics in ALL cells. We used liquid chromatography-mass spectrometry (LC-MS) to quantify MTX and folate polyglutamate levels in folylpoly-γ-glutamate synthetase (FPGS) mutant ALL cells. Enzymatic activity and protein degradation assays were also conducted to characterize the catalytic properties and protein stabilities of FPGS mutants. An ALL cell line-derived mouse leukemia xenograft model was used to evaluate the in vivo impact of FPGS inactivation on leukemogenesis and sensitivity to the polyglutamatable antifolate MTX as well as non-polyglutamatble lipophilic antifolate trimetrexate (TMQ). RESULTS We found a significant decrease in folate polyglutamylation network activities during ALL relapse using RNA-seq data. Supported by functional evidence, we identified multifactorial mechanisms of FPGS inactivation in relapsed ALL, including its decreased network activity and gene expression, focal gene deletion, impaired catalytic activity, and increased protein degradation. These deleterious FPGS alterations induce MTX resistance and inevitably cause marked intracellular folate shrinkage, which could be efficiently targeted by a polyglutamylation-independent lipophilic antifolate TMQ in vitro and in vivo. CONCLUSIONS MTX resistance in relapsed ALL relies on FPGS inactivation, which inevitably induces a folate metabolic vulnerability, allowing for an efficacious antifolate ALL treatment strategy that is based upon TMQ, thereby surmounting chemoresistance in relapsed ALL.
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Affiliation(s)
- Hui Li
- Pediatric Translational Medicine Institute, Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Fujian Children's Hospital, Fujian Branch of Shanghai Children's Medical Center Affiliated to Shanghai Jiao Tong University School of Medicine, Fuzhou, China
| | - Yao Chen
- Pediatric Translational Medicine Institute, Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ming Ding
- Pediatric Translational Medicine Institute, Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jingjing Liu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Huiying Sun
- Pediatric Translational Medicine Institute, Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Houshun Fang
- Pediatric Translational Medicine Institute, Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Samuel W Brady
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yan Xu
- Pediatric Translational Medicine Institute, Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fabian Glaser
- Structural and Computational Biology Unit, The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yabin Tang
- Department of Pharmacology and Chemical Biology, School of Basic Medicine and Shanghai Collaborative Innovation Center for Translational Medicine Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | - Xiaoyu Wu
- Pediatric Translational Medicine Institute, Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuxuan Wang
- Pediatric Translational Medicine Institute, Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Liang Zhu
- Department of Pharmacology and Chemical Biology, School of Basic Medicine and Shanghai Collaborative Innovation Center for Translational Medicine Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Benshang Li
- Pediatric Translational Medicine Institute, Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuhong Shen
- Pediatric Translational Medicine Institute, Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Fujian Children's Hospital, Fujian Branch of Shanghai Children's Medical Center Affiliated to Shanghai Jiao Tong University School of Medicine, Fuzhou, China
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Liang Zheng
- Pediatric Translational Medicine Institute, Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Fujian Children's Hospital, Fujian Branch of Shanghai Children's Medical Center Affiliated to Shanghai Jiao Tong University School of Medicine, Fuzhou, China.
| | - Jiyang Yu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Yehuda G Assaraf
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel.
| | - Bin-Bing S Zhou
- Pediatric Translational Medicine Institute, Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Fujian Children's Hospital, Fujian Branch of Shanghai Children's Medical Center Affiliated to Shanghai Jiao Tong University School of Medicine, Fuzhou, China; Department of Pharmacology and Chemical Biology, School of Basic Medicine and Shanghai Collaborative Innovation Center for Translational Medicine Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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2
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Hwang HW, Shin HT, An HY, Byun JW. Genomic progression for local invasion of cutaneous squamous cell carcinoma from the superficial to the deep portion. Int J Cancer 2024; 155:532-544. [PMID: 38739001 DOI: 10.1002/ijc.34952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 02/29/2024] [Accepted: 03/19/2024] [Indexed: 05/14/2024]
Abstract
Cutaneous squamous cell carcinoma (cSCC) is the second most common skin cancer. While many treatments exist, our understanding of its genomic progression, especially from the epidermis to the deep dermis, remains limited. This study aims to identify genetic mutations associated with the progression of cSCC into the deep dermis, providing insights into its aggressive behavior and high-risk features. We performed high-depth whole-exome sequencing on 12 cSCC tissues, along with paired normal tissues from six patients, using microdissection techniques. The mutational analysis focused on identifying alterations enriched during cSCC progression. Gene Ontology enrichment analysis, immunohistochemical assays, and external single-cell RNA data were utilized for validation. A total of 8863 non-synonymous somatic mutations were identified in 4092 genes across the superficial and deep portions of cSCCs. Analysis of deep portion mutations revealed a significant correlation with gene ontology biological processes, particularly cell junction organization, and cell-cell adhesion. Clonal mutations in these processes were more prevalent in the deep portions, indicating their impact on the cSCC mutation landscape. Genetic evolution analysis identified 29 causal genes associated with dermal invasion in cSCC. We highlight somatic mutations in cSCC, revealing heterogeneity between superficial and deep regions. Altered genes in cell junction organization and cell-cell adhesion emerged as pivotal in dermal invasion. We identified 29 causal genes primarily in deep tumor regions. Our findings emphasize analyzing multiple tumor regions to capture varied mutational landscapes. These insights advance our understanding of cSCC progression, emphasizing genetic and cellular changes during tumor evolution.
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Affiliation(s)
- Hye Won Hwang
- Department of Dermatology, Inha University School of Medicine, Incheon, Republic of Korea
| | - Hyun-Tae Shin
- Department of Dermatology, Inha University School of Medicine, Incheon, Republic of Korea
- Research Center for Controlling Intercellular Communication (RCIC), Inha University School of Medicine, Incheon, Republic of Korea
| | - Hye Young An
- Department of Dermatology, Inha University School of Medicine, Incheon, Republic of Korea
| | - Ji Won Byun
- Department of Dermatology, Inha University School of Medicine, Incheon, Republic of Korea
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3
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Wu CJ, Livak F, Ashwell JD. The histone methyltransferase KMT2D maintains cellular glucocorticoid responsiveness by shielding the glucocorticoid receptor from degradation. J Biol Chem 2024; 300:107581. [PMID: 39025450 DOI: 10.1016/j.jbc.2024.107581] [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: 04/01/2024] [Revised: 07/06/2024] [Accepted: 07/09/2024] [Indexed: 07/20/2024] Open
Abstract
Because of their ability to induce lymphocyte apoptosis, glucocorticoids (GC) are widely used to treat hematological malignancies such as lymphomas and multiple myeloma. Their effectiveness is often limited, however, due to the development of glucocorticoid resistance by a variety of molecular mechanisms. Here we performed an unbiased genome-wide CRISPR screen with the human T-cell leukemia cell line Jurkat to find previously unidentified genes required for GC-induced apoptosis. One such gene was KMT2D (also known as MLL2 or MLL4), which encodes a histone lysine methyltransferase whose mutations are associated with a variety of cancers, blood malignancies in particular, and are considered markers of poor prognosis. Knockout of KMT2D by CRISPR/Cas9 gene editing in Jurkat and several multiple myeloma cell lines downregulated GR protein expression. Surprisingly, this was not due to a reduction in GR transcripts, but rather to a decrease in the protein's half-life, primarily due to proteasomal degradation. Reconstitution of KMT2D expression restored GR levels. In contrast to the known ability of KMT2D to control gene transcription through covalent histone methylation, KMT2D-mediated upregulation of GR levels did not require its methyltransferase activity. Co-immunoprecipitation and proximity ligation assays found constitutive binding of KMT2D to the GR, which was enhanced in the presence of GC. These observations reveal KMT2D to be essential for the stabilization of cellular GR levels, and suggest a possible mechanism by which KMT2D mutations may lead to GC resistance in some malignancies.
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Affiliation(s)
- Chuan-Jin Wu
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Ferenc Livak
- Laboratory of Genome Integrity Flow Cytometry Core, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Jonathan D Ashwell
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA.
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4
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Tandukar B, Deivendran D, Chen L, Cruz-Pacheco N, Sharma H, Xu A, Bandari AK, Chen DB, George C, Marty A, Cho RJ, Cheng J, Saylor D, Gerami P, Arron ST, Bastian BC, Shain AH. Genetic evolution of keratinocytes to cutaneous squamous cell carcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.23.604673. [PMID: 39091884 PMCID: PMC11291049 DOI: 10.1101/2024.07.23.604673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
We performed multi-omic profiling of epidermal keratinocytes, precancerous actinic keratoses, and squamous cell carcinomas to understand the molecular transitions during skin carcinogenesis. Single-cell mutational analyses showed that most keratinocytes in normal skin had lower mutation burdens than melanocytes and fibroblasts, however keratinocytes with TP53 or NOTCH1 mutations had substantially higher mutation burdens, suggesting that these mutations prime keratinocytes for transformation by increasing their mutation rate. Mutational profiling and spatial transcriptomics on squamous cell carcinomas adjacent to actinic keratoses revealed TERT promoter and CDKN2A mutations emerging in actinic keratoses, whereas additional mutations inactivating ARID2 and activating the MAPK-pathway delineated the transition to squamous cell carcinomas. Spatial variation in gene expression patterns was common in both tumor and immune cells, with high expression of checkpoint molecules at the invasive front of tumors. In conclusion, this study documents key events during the evolution of cutaneous squamous cell carcinoma.
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Affiliation(s)
- Bishal Tandukar
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Delahny Deivendran
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Limin Chen
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Noel Cruz-Pacheco
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Harsh Sharma
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Albert Xu
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Aravind K. Bandari
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Daniel B. Chen
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Christopher George
- Department of Dermatology, Erasmus MC, Rotterdam, Netherlands
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Dermatology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Annika Marty
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - Raymond J. Cho
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
| | - Jeffrey Cheng
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
| | - Drew Saylor
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
| | - Pedram Gerami
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | - Boris C. Bastian
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - A. Hunter Shain
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
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5
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Torres-Diz M, Reglero C, Falkenstein CD, Castro A, Hayer KE, Radens CM, Quesnel-Vallières M, Ang Z, Sehgal P, Li MM, Barash Y, Tasian SK, Ferrando A, Thomas-Tikhonenko A. An Alternatively Spliced Gain-of-Function NT5C2 Isoform Contributes to Chemoresistance in Acute Lymphoblastic Leukemia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.14.557413. [PMID: 39091882 PMCID: PMC11291008 DOI: 10.1101/2023.09.14.557413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Relapsed or refractory B-cell acute lymphoblastic leukemia (B-ALL) is a major cause of pediatric cancer-related deaths. Relapse-specific mutations do not account for all chemotherapy failures in B- ALL patients, suggesting additional mechanisms of resistance. By mining RNA-seq datasets of paired diagnostic/relapse pediatric B-ALL samples, we discovered pervasive alternative splicing (AS) patterns linked to relapse and affecting drivers of resistance to glucocorticoids, anti-folates, and thiopurines. Most splicing variations represented cassette exon skipping, "poison" exon inclusion, and intron retention, phenocopying well-documented loss-of-function mutations. In contrast, relapse-associated AS of NT5C2 mRNA yielded an isoform with the functionally uncharacterized in-frame exon 6a. Incorporation of the 8-amino acid sequence SQVAVQKR into this enzyme created a putative phosphorylation site and resulted in elevated nucleosidase activity, which is a known consequence of gain-of-function mutations in NT5C2 and a common determinant of 6-mercaptopurine (6-MP) resistance. Consistent with this finding, NT5C2ex6a and the R238W hotspot variant conferred comparable levels of resistance to 6-MP in B-ALL cells both in vitro and in vivo. Furthermore, both the NT5C2ex6a and R238W variants induced collateral sensitivity to the inosine monophosphate dehydrogenase (IMPDH) inhibitor mizoribine. These results ascribe an important role for splicing perturbations in chemotherapy resistance in relapsed B-ALL and suggest that IMPDH inhibitors, including the commonly used immunosuppressive agent mycophenolate mofetil, could be a valuable therapeutic option for treating thiopurine-resistant leukemias.
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6
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Flynn A, Waszak SM, Weischenfeldt J. Somatic CpG hypermutation is associated with mismatch repair deficiency in cancer. Mol Syst Biol 2024:10.1038/s44320-024-00054-5. [PMID: 39026103 DOI: 10.1038/s44320-024-00054-5] [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: 12/07/2023] [Revised: 06/17/2024] [Accepted: 06/28/2024] [Indexed: 07/20/2024] Open
Abstract
Somatic hypermutation in cancer has gained momentum with the increased use of tumour mutation burden as a biomarker for immune checkpoint inhibitors. Spontaneous deamination of 5-methylcytosine to thymine at CpG dinucleotides is one of the most ubiquitous endogenous mutational processes in normal and cancer cells. Here, we performed a systematic investigation of somatic CpG hypermutation at a pan-cancer level. We studied 30,191 cancer patients and 103 cancer types and developed an algorithm to identify somatic CpG hypermutation. Across cancer types, we observed the highest prevalence in paediatric leukaemia (3.5%), paediatric high-grade glioma (1.7%), and colorectal cancer (1%). We discovered germline variants and somatic mutations in the mismatch repair complex MutSα (MSH2-MSH6) as genetic drivers of somatic CpG hypermutation in cancer, which frequently converged on CpG sites and TP53 driver mutations. We further observe an association between somatic CpG hypermutation and response to immune checkpoint inhibitors. Overall, our study identified novel cancer types that display somatic CpG hypermutation, strong association with MutSα-deficiency, and potential utility in cancer immunotherapy.
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Affiliation(s)
- Aidan Flynn
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- The Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Parkville, VIC, Australia
| | - Sebastian M Waszak
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
- Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway.
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
| | - Joachim Weischenfeldt
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.
- The Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark.
- The DCCC Brain Tumor Center, Danish Comprehensive Cancer Center, Copenhagen, Denmark.
- Department of Urology, Charité University Hospital, Berlin, Germany.
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7
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Bertrums EJM, de Kanter JK, Derks LLM, Verheul M, Trabut L, van Roosmalen MJ, Hasle H, Antoniou E, Reinhardt D, Dworzak MN, Mühlegger N, van den Heuvel-Eibrink MM, Zwaan CM, Goemans BF, van Boxtel R. Selective pressures of platinum compounds shape the evolution of therapy-related myeloid neoplasms. Nat Commun 2024; 15:6025. [PMID: 39019934 PMCID: PMC11255340 DOI: 10.1038/s41467-024-50384-z] [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: 06/12/2023] [Accepted: 07/08/2024] [Indexed: 07/19/2024] Open
Abstract
Therapy-related myeloid neoplasms (t-MN) arise as a complication of chemo- and/or radiotherapy. Although t-MN can occur both in adult and childhood cancer survivors, the mechanisms driving therapy-related leukemogenesis likely vary across different ages. Chemotherapy is thought to induce driver mutations in children, whereas in adults pre-existing mutant clones are selected by the exposure. However, selective pressures induced by chemotherapy early in life are less well studied. Here, we use single-cell whole genome sequencing and phylogenetic inference to show that the founding cell of t-MN in children starts expanding after cessation of platinum exposure. In patients with Li-Fraumeni syndrome, characterized by a germline TP53 mutation, we find that the t-MN already expands during treatment, suggesting that platinum-induced growth inhibition is TP53-dependent. Our results demonstrate that germline aberrations can interact with treatment exposures in inducing t-MN, which is important for the development of more targeted, patient-specific treatment regimens and follow-up.
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Affiliation(s)
- Eline J M Bertrums
- Princess Máxima Centrum for pediatric oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
- Department of Pediatric Oncology/Hematology, Erasmus Medical Center - Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Jurrian K de Kanter
- Princess Máxima Centrum for pediatric oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Lucca L M Derks
- Princess Máxima Centrum for pediatric oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Mark Verheul
- Princess Máxima Centrum for pediatric oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Laurianne Trabut
- Princess Máxima Centrum for pediatric oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Markus J van Roosmalen
- Princess Máxima Centrum for pediatric oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Henrik Hasle
- Department of Pediatrics, Aarhus University Hospital, Aarhus, Denmark
| | - Evangelia Antoniou
- Clinic of Pediatrics III, University Hospital of Essen, Essen, Germany
- AML-BFM Study Group, Essen, Germany
| | - Dirk Reinhardt
- Clinic of Pediatrics III, University Hospital of Essen, Essen, Germany
- AML-BFM Study Group, Essen, Germany
| | - Michael N Dworzak
- St. Anna Children's Cancer Research Institute, Vienna, Austria
- St. Anna Children's Hospital, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Nora Mühlegger
- St. Anna Children's Cancer Research Institute, Vienna, Austria
| | | | - C Michel Zwaan
- Princess Máxima Centrum for pediatric oncology, Utrecht, the Netherlands
- Department of Pediatric Oncology/Hematology, Erasmus Medical Center - Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Bianca F Goemans
- Princess Máxima Centrum for pediatric oncology, Utrecht, the Netherlands
| | - Ruben van Boxtel
- Princess Máxima Centrum for pediatric oncology, Utrecht, the Netherlands.
- Oncode Institute, Utrecht, the Netherlands.
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8
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Mohd Nippah NF, Abu N, Ab Mutalib NS, Alias H. Advances in next-generation sequencing for relapsed pediatric acute lymphoblastic leukemia: current insights and future directions. Front Genet 2024; 15:1394523. [PMID: 38894724 PMCID: PMC11183504 DOI: 10.3389/fgene.2024.1394523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 05/17/2024] [Indexed: 06/21/2024] Open
Abstract
Leukemia is one of the most common cancers in children; and its genetic diversity in the landscape of acute lymphoblastic leukemia (ALL) is important for diagnosis, risk assessment, and therapeutic approaches. Relapsed ALL remains the leading cause of cancer deaths among children. Almost 20% of children who are treated for ALL and achieve complete remission experience disease recurrence. Relapsed ALL has a poor prognosis, and relapses are more likely to have mutations that affect signaling pathways, chromatin patterning, tumor suppression, and nucleoside metabolism. The identification of ALL subtypes has been based on genomic alterations for several decades, using the molecular landscape at relapse and its clinical significance. Next-generation sequencing (NGS), also known as massive parallel sequencing, is a high-throughput, quick, accurate, and sensitive method to examine the molecular landscape of cancer. This has undoubtedly transformed the study of relapsed ALL. The implementation of NGS has improved ALL genomic analysis, resulting in the recent identification of various novel molecular entities and a deeper understanding of existing ones. Thus, this review aimed to consolidate and critically evaluate the most current information on relapsed pediatric ALL provided by NGS technology. In this phase of targeted therapy and personalized medicine, identifying the capabilities, benefits, and drawbacks of NGS will be essential for healthcare professionals and researchers offering genome-driven care. This would contribute to precision medicine to treat these patients and help improve their overall survival and quality of life.
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Affiliation(s)
- Nur Farhana Mohd Nippah
- Department of Pediatrics, Faculty of Medicine, National University of Malaysia, Kuala Lumpur, Malaysia
| | - Nadiah Abu
- UKM Medical Molecular Biology Institute (UMBI), National University of Malaysia, Kuala Lumpur, Malaysia
| | - Nurul Syakima Ab Mutalib
- UKM Medical Molecular Biology Institute (UMBI), National University of Malaysia, Kuala Lumpur, Malaysia
| | - Hamidah Alias
- Department of Pediatrics, Faculty of Medicine, National University of Malaysia, Kuala Lumpur, Malaysia
- UKM Medical Molecular Biology Institute (UMBI), National University of Malaysia, Kuala Lumpur, Malaysia
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9
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Nguyen T, Aida T, Iijima‐Yamashita Y, Tamai M, Nagamachi A, Kagami K, Komatsu C, Kasai S, Akahane K, Goi K, Inaba T, Sanada M, Inukai T. Application of prime editing system to introduce TP53 R248Q hotspot mutation in acute lymphoblastic leukemia cell line. Cancer Sci 2024; 115:1924-1935. [PMID: 38549229 PMCID: PMC11145152 DOI: 10.1111/cas.16162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 03/08/2024] [Accepted: 03/11/2024] [Indexed: 06/04/2024] Open
Abstract
In childhood acute lymphoblastic leukemia (ALL), TP53 gene mutation is associated with chemoresistance in a certain population of relapsed cases. To directly verify the association of TP53 gene mutation with chemoresistance of relapsed childhood ALL cases and improve their prognosis, the development of appropriate human leukemia models having TP53 mutation in the intrinsic gene is required. Here, we sought to introduce R248Q hotspot mutation into the intrinsic TP53 gene in an ALL cell line, 697, by applying a prime editing (PE) system, which is a versatile genome editing technology. The PE2 system uses an artificial fusion of nickase Cas9 and reverse-transcriptase to directly place new genetic information into a target site through a reverse transcriptase template in the prime editing guide RNA (pegRNA). Moreover, in the advanced PE3b system, single guide RNA (sgRNA) matching the edited sequence is also introduced to improve editing efficiency. The initially obtained MDM2 inhibitor-resistant PE3b-transfected subline revealed disrupted p53 transactivation activity, reduced p53 target gene expression, and acquired resistance to chemotherapeutic agents and irradiation. Although the majority of the subline acquired the designed R248Q and adjacent silent mutations, the insertion of the palindromic sequence in the scaffold hairpin structure of pegRNA and the overlap of the original genomic DNA sequence were frequently observed. Targeted next-generation sequencing reconfirmed frequent edit errors in both PE2 and PE3b-transfected 697 cells, and it revealed frequent successful edits in HEK293T cells. These observations suggest a requirement for further modification of the PE2 and PE3b systems for accurate editing in leukemic cells.
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Affiliation(s)
- Thao Nguyen
- Department of Pediatrics, School of MedicineUniversity of YamanashiChuoJapan
| | - Tomomi Aida
- McGovern Institute for Brain ResearchMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Yuka Iijima‐Yamashita
- Department of Advanced DiagnosisClinical Research Center, NHO Nagoya Medical CenterNagoyaJapan
| | - Minori Tamai
- Department of Pediatrics, School of MedicineUniversity of YamanashiChuoJapan
| | - Akiko Nagamachi
- Department of Molecular Oncology and Leukemia Program ProjectResearch Institute for Radiation Biology and Medicine, Hiroshima UniversityHigashihiroshimaJapan
| | - Keiko Kagami
- Department of Pediatrics, School of MedicineUniversity of YamanashiChuoJapan
| | - Chiaki Komatsu
- Department of Pediatrics, School of MedicineUniversity of YamanashiChuoJapan
| | - Shin Kasai
- Department of Pediatrics, School of MedicineUniversity of YamanashiChuoJapan
| | - Koshi Akahane
- Department of Pediatrics, School of MedicineUniversity of YamanashiChuoJapan
| | - Kumiko Goi
- Department of Pediatrics, School of MedicineUniversity of YamanashiChuoJapan
| | - Toshiya Inaba
- Department of Molecular Oncology and Leukemia Program ProjectResearch Institute for Radiation Biology and Medicine, Hiroshima UniversityHigashihiroshimaJapan
| | - Masashi Sanada
- Department of Advanced DiagnosisClinical Research Center, NHO Nagoya Medical CenterNagoyaJapan
| | - Takeshi Inukai
- Department of Pediatrics, School of MedicineUniversity of YamanashiChuoJapan
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10
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Chen X, Yang W, Roberts CWM, Zhang J. Developmental origins shape the paediatric cancer genome. Nat Rev Cancer 2024; 24:382-398. [PMID: 38698126 DOI: 10.1038/s41568-024-00684-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/18/2024] [Indexed: 05/05/2024]
Abstract
In the past two decades, technological advances have brought unprecedented insights into the paediatric cancer genome revealing characteristics distinct from those of adult cancer. Originating from developing tissues, paediatric cancers generally have low mutation burden and are driven by variants that disrupt the transcriptional activity, chromatin state, non-coding cis-regulatory regions and other biological functions. Within each tumour, there are multiple populations of cells with varying states, and the lineages of some can be tracked to their fetal origins. Genome-wide genetic screening has identified vulnerabilities associated with both the cell of origin and transcription deregulation in paediatric cancer, which have become a valuable resource for designing new therapeutic approaches including those for small molecules, immunotherapy and targeted protein degradation. In this Review, we present recent findings on these facets of paediatric cancer from a pan-cancer perspective and provide an outlook on future investigations.
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Affiliation(s)
- Xiaolong Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wentao Yang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles W M Roberts
- Comprehensive Cancer Center, St Jude Children's Research Hospital, Memphis, TN, USA
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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11
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Li X, Lin S, Liao N, Mai H, Long X, Liu L, Wu B, Chen Q, Kong Q, Kong X, Liu L, Qin J, Fang J, Zhou D. The RAS-signaling-pathway-mutation-related prognosis in B-cell acute lymphoblastic leukemia: A report from South China children's leukemia group. Hematol Oncol 2024; 42:e3265. [PMID: 38564328 DOI: 10.1002/hon.3265] [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: 07/03/2023] [Revised: 01/24/2024] [Accepted: 02/23/2024] [Indexed: 04/04/2024]
Abstract
The next-generation sequencing technologies application discovers novel genetic alterations frequently in pediatric acute lymphoblastic leukemia (ALL). RAS signaling pathway mutations at the time of relapse ALL frequently appear as small subclones at the time of onset, which are considered as the drivers in ALL relapse. Whether subclones alterations in the RAS signaling pathway should be considered for risk group stratification of ALL treatment is not decided yet. In this work, we investigate the RAS signaling pathway mutation spectrum and the related prognosis in pediatric ALL. We employed an NGS panel comprising 220 genes. NGS results were collected from 202 pediatric ALL patients. 155 patients (76.7%) harbored at least one mutation. The incidences of RAS signaling pathway mutations are different significantly between T-ALL and B-ALL. In B-ALL, the RAS pathway is mostly involved, and NRAS (17.6%), KRAS (22.7%), and PTPN11 (7.7%) were the three most frequently mutated genes. Co-occurring mutations of CREBBP and NRAS, FLT3, or PTPN11 (p = 0.002, p = 0.009, and p = 0.003, respectively) were found in this cohort. The 3-year RFS rates for the RAS signaling pathway mutation-positive and negative cases was 76.5 % versus 89.7 % (p = 0.012). Four cases relapsed in the lately 3 years were RAS signaling pathway mutation-positive. RAS signaling pathway mutation is an important biomarker for poorer relapse-free survival in pediatric B-ALL patients despite good early MRD levels.
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Affiliation(s)
- Xinyu Li
- Department of Pediatric Hematology/Oncology, Children's Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shaofen Lin
- Department of Pediatric Hematology/Oncology, Children's Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ning Liao
- Department of Pediatrics, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Huirong Mai
- Department of Hematology and Oncology, Shenzhen Children's Hospital, Shenzhen, China
| | - Xingjiang Long
- Department of Pediatrics, Liuzhou People's Hospital, Liuzhou, China
| | - Lili Liu
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Beiyan Wu
- Department of Pediatrics, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Qiwen Chen
- Department of Pediatrics, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Qian Kong
- Department of Pediatrics, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xianling Kong
- Department of Pediatrics, Boai Hospital of Zhongshan, Zhongshan, China
| | - Lixia Liu
- Department of Medical Affairs, Acornmed Biotechnology Co., Ltd., Tianjin, China
| | - Jiayue Qin
- Department of Medical Affairs, Acornmed Biotechnology Co., Ltd., Tianjin, China
| | - Jianpei Fang
- Department of Pediatric Hematology/Oncology, Children's Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Dunhua Zhou
- Department of Pediatric Hematology/Oncology, Children's Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
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12
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Van Hulst AM, Van der Zwet JCG, Buijs-Gladdines JGCAM, Smits WK, Fiocco M, Pieters R, Van Leeuwen FN, Van den Heuvel-Eibrink MM, Van den Akker ELT, Meijerink JPP. The role of the mineralocorticoid receptor in steroidinduced cytotoxicity in pediatric acute lymphoblastic leukemia. Haematologica 2024; 109:1551-1556. [PMID: 38205521 PMCID: PMC11063837 DOI: 10.3324/haematol.2023.282928] [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: 02/10/2023] [Accepted: 01/02/2024] [Indexed: 01/12/2024] Open
Abstract
Not available.
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Affiliation(s)
| | | | | | | | - Marta Fiocco
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands; Mathematical Institute, Leiden University, Leiden, The Netherlands; Department of Biomedical data Science, Medical Statistics, Leiden University Medical Centre
| | - Rob Pieters
- Princess Maxima Center for Pediatric Oncology, Utrecht
| | | | - Marry M Van den Heuvel-Eibrink
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands; Child Health, UMCU-Wilhelmina Children's Hospital, Utrecht.
| | | | - Jules P P Meijerink
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands; Presently working at Acerta-Pharma (AstraZeneca), Oss
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13
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Wilke N, Frias C, Berkessel A, Prokop A. (2,6-Dimethylphenyl)arsonic Acid Induces Apoptosis through the Mitochondrial Pathway, Downregulates XIAP, and Overcomes Multidrug Resistance to Cytostatic Drugs in Leukemia and Lymphoma Cells In Vitro. Int J Mol Sci 2024; 25:4713. [PMID: 38731935 PMCID: PMC11083614 DOI: 10.3390/ijms25094713] [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: 03/16/2024] [Revised: 04/13/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024] Open
Abstract
Cancer treatment is greatly challenged by drug resistance, highlighting the need for novel drug discoveries. Here, we investigated novel organoarsenic compounds regarding their resistance-breaking and apoptosis-inducing properties in leukemia and lymphoma. Notably, the compound (2,6-dimethylphenyl)arsonic acid (As2) demonstrated significant inhibition of cell proliferation and induction of apoptosis in leukemia and lymphoma cells while sparing healthy leukocytes. As2 reached half of its maximum activity (AC50) against leukemia cells at around 6.3 µM. Further experiments showed that As2 overcomes multidrug resistance and sensitizes drug-resistant leukemia and lymphoma cell lines to treatments with the common cytostatic drugs vincristine, daunorubicin, and cytarabine at low micromolar concentrations. Mechanistic investigations of As2-mediated apoptosis involving FADD (FAS-associated death domain)-deficient or Smac (second mitochondria-derived activator of caspases)/DIABLO (direct IAP binding protein with low pI)-overexpressing cell lines, western blot analysis of caspase-9 cleavage, and measurements of mitochondrial membrane integrity identified the mitochondrial apoptosis pathway as the main mode of action. Downregulation of XIAP (x-linked inhibitor of apoptosis protein) and apoptosis induction independent of Bcl-2 (B-cell lymphoma 2) and caspase-3 expression levels suggest the activation of additional apoptosis-promoting mechanisms. Due to the selective apoptosis induction, the synergistic effects with common anti-cancer drugs, and the ability to overcome multidrug resistance in vitro, As2 represents a promising candidate for further preclinical investigations with respect to refractory malignancies.
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Affiliation(s)
- Nathalie Wilke
- Department of Pediatric Hematology/Oncology, Children’s Hospital Cologne, Amsterdamer Straße 59, 50735 Cologne, Germany
| | - Corazon Frias
- Department of Pediatric Hematology/Oncology, Children’s Hospital Cologne, Amsterdamer Straße 59, 50735 Cologne, Germany
- Department of Pediatric Oncology/Hematology, Helios Clinics Schwerin, Wismarsche Straße 393–397, 19049 Schwerin, Germany
- Medical School Hamburg (MSH), University of Applied Sciences and Medical University, Am Kaiserkai 1, 20457 Hamburg, Germany
| | - Albrecht Berkessel
- Department of Chemistry, Organic Chemistry, University of Cologne, Greinstraße 4, 50939 Cologne, Germany
| | - Aram Prokop
- Department of Pediatric Hematology/Oncology, Children’s Hospital Cologne, Amsterdamer Straße 59, 50735 Cologne, Germany
- Department of Pediatric Oncology/Hematology, Helios Clinics Schwerin, Wismarsche Straße 393–397, 19049 Schwerin, Germany
- Medical School Hamburg (MSH), University of Applied Sciences and Medical University, Am Kaiserkai 1, 20457 Hamburg, Germany
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14
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Gong X, Hu T, Shen Q, Zhang L, Zhang W, Liu X, Zong S, Li X, Wang T, Yan W, Hu Y, Chen X, Zheng J, Zhang A, Wang J, Feng Y, Li C, Ma J, Gao X, Song Z, Zhang Y, Gale RP, Zhu X, Chen J. Gene expression prognostic of early relapse risk in low-risk B-cell acute lymphoblastic leukaemia in children. EJHAEM 2024; 5:333-345. [PMID: 38633121 PMCID: PMC11020147 DOI: 10.1002/jha2.872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 02/21/2024] [Indexed: 04/19/2024]
Abstract
ETV6::RUNX1 is the most common fusion gene in childhood acute lymphoblastic leukaemia (ALL) and is associated with favorable outcomes, especially in low-risk children. However, as many as 10% of children relapse within 3 years, and such early relapses have poor survival. Identifying children at risk for early relapse is an important challenge. We interrogated data from 87 children with low-risk ETV6::RUNX1-positive B-cell ALL and with available preserved bone marrow samples (discovery cohort). We profiled somatic point mutations in a panel of 559 genes and genome-wide transcriptome and single-nucleotide variants. We found high TIMD4 expression (> 85th-percentile value) at diagnosis was the most important independent prognostic factor of early relapse (hazard ratio [HR] = 5.07 [1.76, 14.62]; p = 0.03). In an independent validation cohort of low-risk ETV6::RUNX1-positive B-cell ALL (N = 68) high TIMD4 expression at diagnosis had an HR = 4.78 [1.07, 21.36] (p = 0.04) for early relapse. In another validation cohort including 78 children with low-risk ETV6::RUNX1-negative B-cell ALL, high TIMD4 expression at diagnosis had an HR = 3.93 [1.31, 11.79] (p = 0.01). Our results suggest high TIMD4 expression at diagnosis in low-risk B-cell ALL in children might be associated with high risk for early relapse.
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15
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Du S, Huang X, He X, Mao M, Chen M, Zhang R, Shao H, Lv Z, Liu X, Chuan J. Association of NUDT15 gene polymorphism with adverse reaction, treatment efficacy, and dose of 6-mercaptopurine in patients with acute lymphoblastic leukemia: a systematic review and meta-analysis. Haematologica 2024; 109:1053-1068. [PMID: 37794799 PMCID: PMC10985454 DOI: 10.3324/haematol.2023.282761] [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: 01/18/2023] [Accepted: 10/26/2023] [Indexed: 10/06/2023] Open
Abstract
6-mercaptopurine (6-MP) serves as the backbone in the maintenance regimens of acute lymphoblastic leukemia (ALL). We aimed to evaluate the influence of NUDT15 gene polymorphism on the risk of myelosupression, hepatotoxicity and interruption of 6-MP, as well as treatment efficacy and dose of 6-MP in ALL patients. A total of 24 studies with 3,374 patients were included in this meta-analysis. We found 9-fold higher risk of 6-MP induced leukopenia (odds ratio [OR] =9.00, 95% confidence interval [CI]: 3.73-21.74) and 2.5-fold higher risk of 6-MP-induced neutropenia (OR=2.52, 95% CI: 1.72-3.69) for NUDT15 c.415C>T variant carriers in the dominant model. Moreover, we found that the dose intensity of 6-MP in ALL patients with one NUDT15 c.415C>T variant alleles (CT) was 19% less than that in wild-type patients (CC) (mean differences: 19.43%, 95% CI: -25.36 to -13.51). The tolerable dose intensity of 6-MP in NUDT15 c.415C>T homozygote variant (TT) and heterozygote variant (CT) carriers was 49% and 15% less than that in wild-type patients, respectively. The NUDT15 c.415C>T variant group (CT+TT) had seven times (OR=6.98, 95% CI: 2.83-17.22) higher risk of developing 6-MP intolerance than the CC group. However, NUDT15 c.415C>T polymorphism did not appear significantly associated with hepatotoxicity, treatment interruption or relapse incidence. We concluded that NUDT15 c.415C>T was a good predictor for 6-MP-induced myelosuppression in ALL patients. The dose intensity of 6-MP in ALL patients with NUDT15 c.415C>T variants was significantly lower than that in wild-type patients. This research provided a basis for further investigation into relations between NUDT15 gene and adverse reaction, treatment efficacy and dose intensity of 6-MP.
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Affiliation(s)
- Shan Du
- Department of Pharmacy, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, China; Personalized Drug Therapy Key Laboratory of Sichuan Province, School of Medicine, University of Electronic Science and Technology of China, Chengdu
| | - Xuefei Huang
- Department of Pharmacy, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, China; Personalized Drug Therapy Key Laboratory of Sichuan Province, School of Medicine, University of Electronic Science and Technology of China, Chengdu
| | - Xia He
- Department of Pharmacy, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, China; Personalized Drug Therapy Key Laboratory of Sichuan Province, School of Medicine, University of Electronic Science and Technology of China, Chengdu
| | - Mian Mao
- Department of Pharmacy, Sichuan Cancer Hospital, Chengdu
| | - Min Chen
- Department of Pharmacy, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, China; Personalized Drug Therapy Key Laboratory of Sichuan Province, School of Medicine, University of Electronic Science and Technology of China, Chengdu
| | - Rong Zhang
- Department of Pediatrics, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu
| | - Huikai Shao
- Department of Pharmacy, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, China; Personalized Drug Therapy Key Laboratory of Sichuan Province, School of Medicine, University of Electronic Science and Technology of China, Chengdu
| | - Ziyan Lv
- Department of Pharmacy, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, China; Personalized Drug Therapy Key Laboratory of Sichuan Province, School of Medicine, University of Electronic Science and Technology of China, Chengdu
| | - Xinxia Liu
- Department of Pharmacy, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, China; Personalized Drug Therapy Key Laboratory of Sichuan Province, School of Medicine, University of Electronic Science and Technology of China, Chengdu.
| | - Junlan Chuan
- Department of Pharmacy, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, China; Personalized Drug Therapy Key Laboratory of Sichuan Province, School of Medicine, University of Electronic Science and Technology of China, Chengdu.
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16
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Dong N, Ma HX, Liu XQ, Li D, Liu LH, Shi Q, Ju XL. Histidine re-sensitizes pediatric acute lymphoblastic leukemia to 6-mercaptopurine through tetrahydrofolate consumption and SIRT5-mediated desuccinylation. Cell Death Dis 2024; 15:216. [PMID: 38485947 PMCID: PMC10940622 DOI: 10.1038/s41419-024-06599-5] [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: 08/31/2023] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 03/18/2024]
Abstract
Despite progressive improvements in the survival rate of pediatric B-cell lineage acute lymphoblastic leukemia (B-ALL), chemoresistance-induced disease progression and recurrence still occur with poor prognosis, thus highlighting the urgent need to eradicate drug resistance in B-ALL. The 6-mercaptopurine (6-MP) is the backbone of ALL combination chemotherapy, and resistance to it is crucially related to relapse. The present study couples chemoresistance in pediatric B-ALL with histidine metabolism deficiency. Evidence was provided that histidine supplementation significantly shifts the 6-MP dose-response in 6-MP-resistant B-ALL. It is revealed that increased tetrahydrofolate consumption via histidine catabolism partially explains the re-sensitization ability of histidine. More importantly, this work provides fresh insights into that desuccinylation mediated by SIRT5 is an indispensable and synergistic requirement for histidine combination therapy against 6-MP resistance, which is undisclosed previously and demonstrates a rational strategy to ameliorate chemoresistance and protect pediatric patients with B-ALL from disease progression or relapse.
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Affiliation(s)
- Na Dong
- Department of Pediatrics, Qilu Hospital of Shandong University, Jinan, 250012, Shandong Province, China
| | - Hui-Xian Ma
- Cryomedicine Laboratory, Qilu Hospital of Shandong University, Jinan, 250012, Shandong Province, China
| | - Xue-Qin Liu
- Department of Pediatrics, Qilu Hospital of Shandong University, Jinan, 250012, Shandong Province, China
| | - Dong Li
- Cryomedicine Laboratory, Qilu Hospital of Shandong University, Jinan, 250012, Shandong Province, China
| | - Ling-Hong Liu
- Cryomedicine Laboratory, Qilu Hospital of Shandong University, Jinan, 250012, Shandong Province, China
| | - Qing Shi
- Cryomedicine Laboratory, Qilu Hospital of Shandong University, Jinan, 250012, Shandong Province, China
| | - Xiu-Li Ju
- Department of Pediatrics, Qilu Hospital of Shandong University, Jinan, 250012, Shandong Province, China.
- Cryomedicine Laboratory, Qilu Hospital of Shandong University, Jinan, 250012, Shandong Province, China.
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17
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Tan RZ. Tumour Growth Mechanisms Determine Effectiveness of Adaptive Therapy in Glandular Tumours. Interdiscip Sci 2024; 16:73-90. [PMID: 37776475 DOI: 10.1007/s12539-023-00586-8] [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: 03/02/2023] [Revised: 09/03/2023] [Accepted: 09/06/2023] [Indexed: 10/02/2023]
Abstract
In cancer treatment, adaptive therapy holds promise for delaying the onset of recurrence through regulating the competition between drug-sensitive and drug-resistant cells. Adaptive therapy has been studied in well-mixed models assuming free mixing of all cells and spatial models considering the interactions of single cells with their immediate adjacent cells. Both models do not reflect the spatial structure in glandular tumours where intra-gland cellular interaction is high, while inter-gland interaction is limited. Here, we use mathematical modelling to study the effects of adaptive therapy on glandular tumours that expand using either glandular fission or invasive growth. A two-dimensional, lattice-based model of sites containing sensitive and resistant cells within individual glands is developed to study the evolution of glandular tumour cells under continuous and adaptive therapies. We found that although both growth models benefit from adaptive therapy's ability to prevent recurrence, invasive growth benefits more from it than fission growth. This difference is due to the migration of daughter cells into neighboring glands that is absent in fission but present in invasive growth. The migration resulted in greater mixing of cells, enhancing competition induced by adaptive therapy. By varying the initial spatial spread and location of the resistant cells within the tumour, we found that modifying the conditions within the resistant cells containing glands affect both fission and invasive growth. However, modifying the conditions surrounding these glands affect invasive growth only. Our work reveals the interplay between growth mechanism and tumour topology in modulating the effectiveness of cancer therapy.
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Affiliation(s)
- Rui Zhen Tan
- Engineering Cluster, Singapore Institute of Technology, 10 Dover Drive, Singapore, 138683, Singapore.
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18
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Sun S, Cheng Y, Hou W, Yan Y, Meng T, Li H, Xiao N. Etoposide-induced SENP8 confers a feed-back drug resistance on acute lymphoblastic leukemia cells. Biochem Biophys Rep 2024; 37:101650. [PMID: 38314144 PMCID: PMC10837060 DOI: 10.1016/j.bbrep.2024.101650] [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: 07/31/2023] [Revised: 12/19/2023] [Accepted: 01/16/2024] [Indexed: 02/06/2024] Open
Abstract
Chemotherapy is the most common treatment for acute lymphoblastic leukemia (ALL). However, many ALL patients eventually develop relapse and treating relapsed ALL has always been challenging. Therefore, exploring the resistance mechanism of chemotherapeutic drugs and proposing feasible intervention strategies are of great significance for ALL treatment. Here, we show that SENP8, whose coding protein is an important deNEDDylase targeting the substrate for deNEDDylation, is highly expressed in relapsed ALL specimens. Interestingly, overexpressing SENP8 specifically reduces the chemosensitivity of ALL cells to etoposide (VP-16) and significantly alleviates the proapoptotic effect of VP-16 on ALL cells. By contrast, NEDDylation inhibition reduces the chemosensitivity of ALL cells to VP-16. Furthermore, VP-16 induces SENP8 accumulation and the instability of MDM2 as well as the stabilization of p53 in ALL cells, and SENP8 knockdown can sensitize ALL cells to VP-16. Our study reveals a novel function of SENP8 in ALL and that VP-16-induced SENP8 confers a feed-back drug resistance on ALL cells, suggesting a possibility of overcoming the chemotherapeutic resistance to VP-16 via targeting SENP8.
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Affiliation(s)
- Shuzhang Sun
- Clinical Research Center, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yixuan Cheng
- Clinical Research Center, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Wanxin Hou
- Department of Oncology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yinjie Yan
- Department of Orthopaedics, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Tian Meng
- Department of Breast Surgery, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hegen Li
- Department of Oncology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ning Xiao
- Clinical Research Center, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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19
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Kolekar P, Balagopal V, Dong L, Liu Y, Foy S, Tran Q, Mulder H, Huskey AL, Plyler E, Liang Z, Ma J, Nakitandwe J, Gu J, Namwanje M, Maciaszek J, Payne-Turner D, Mallampati S, Wang L, Easton J, Klco JM, Ma X. SJPedPanel: A pan-cancer gene panel for childhood malignancies. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.11.27.23299068. [PMID: 38076942 PMCID: PMC10705664 DOI: 10.1101/2023.11.27.23299068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Background Large scale genomics projects have identified driver alterations for most childhood cancers that provide reliable biomarkers for clinical diagnosis and disease monitoring using targeted sequencing. However, there is lack of a comprehensive panel that matches the list of known driver genes. Here we fill this gap by developing SJPedPanel for childhood cancers. Results SJPedPanel covers 5,275 coding exons of 357 driver genes, 297 introns frequently involved in rearrangements that generate fusion oncoproteins, commonly amplified/deleted regions (e.g., MYCN for neuroblastoma, CDKN2A and PAX5 for B-/T-ALL, and SMARCB1 for AT/RT), and 7,590 polymorphism sites for interrogating tumors with aneuploidy, such as hyperdiploid and hypodiploid B-ALL or 17q gain neuroblastoma. We used driver alterations reported from an established real-time clinical genomics cohort (n=253) to validate this gene panel. Among the 485 pathogenic variants reported, our panel covered 417 variants (86%). For 90 rearrangements responsible for oncogenic fusions, our panel covered 74 events (82%). We re-sequenced 113 previously characterized clinical specimens at an average depth of 2,500X using SJPedPanel and recovered 354 (91%) of the 389 reported pathogenic variants. We then investigated the power of this panel in detecting mutations from specimens with low tumor purity (as low as 0.1%) using cell line-based dilution experiments and discovered that this gene panel enabled us to detect ∼80% variants with allele fraction of 0.2%, while the detection rate decreases to ∼50% when the allele fraction is 0.1%. We finally demonstrate its utility in disease monitoring on clinical specimens collected from AML patients in morphologic remission. Conclusions SJPedPanel enables the detection of clinically relevant genetic alterations including rearrangements responsible for subtype-defining fusions for childhood cancers by targeted sequencing of ∼0.15% of human genome. It will enhance the analysis of specimens with low tumor burdens for cancer monitoring and early detection.
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20
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Chen Y, Fang H, Sun H, Wu X, Xu Y, Zhou BBS, Li H. Up-regulation of ABCG1 is associated with methotrexate resistance in acute lymphoblastic leukemia cells. Front Pharmacol 2024; 14:1331687. [PMID: 38259297 PMCID: PMC10800869 DOI: 10.3389/fphar.2023.1331687] [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: 11/01/2023] [Accepted: 12/18/2023] [Indexed: 01/24/2024] Open
Abstract
Acute lymphoblastic leukemia (ALL) is a prevalent hematologic malignancy in children, and methotrexate (MTX) is a widely employed curative treatment. Despite its common use, clinical resistance to MTX is frequently encountered. In this study, an MTX-resistant cell line (Reh-MTXR) was established through a stepwise selection process from the ALL cell line Reh. Comparative analysis revealed that Reh-MTXR cells exhibited resistance to MTX in contrast to the parental Reh cells. RNA-seq analysis identified an upregulation of ATP-binding cassette transporter G1 (ABCG1) in Reh-MTXR cells. Knockdown of ABCG1 in Reh-MTXR cells reversed the MTX-resistant phenotype, while overexpression of ABCG1 in Reh cells conferred resistance to MTX. Mechanistically, the heightened expression of ABCG1 accelerated MTX efflux, leading to a reduced accumulation of MTX polyglutamated metabolites. Notably, the ABCG1 inhibitor benzamil effectively sensitized Reh-MTXR cells to MTX treatment. Moreover, the observed upregulation of ABCG1 in Reh-MTXR cells was not induced by alterations in DNA methylation or histone acetylation. This study provides insight into the mechanistic basis of MTX resistance in ALL and also suggests a potential therapeutic approach for MTX-resistant ALL in the future.
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Affiliation(s)
- Yao Chen
- Pediatric Translational Medicine Institute, Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Houshun Fang
- Pediatric Translational Medicine Institute, Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huiying Sun
- Pediatric Translational Medicine Institute, Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaoyu Wu
- Pediatric Translational Medicine Institute, Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yan Xu
- Pediatric Translational Medicine Institute, Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bin-Bing S. Zhou
- Pediatric Translational Medicine Institute, Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Fujian Children’s Hospital, Fujian Branch of Shanghai Children’s Medical Center Affiliated to Shanghai Jiaotong University School of Medicine, Fuzhou, China
- Department of Pharmacology and Chemical Biology, School of Basic Medicine and Shanghai Collaborative Innovation Center for Translational Medicine Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hui Li
- Pediatric Translational Medicine Institute, Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Fujian Children’s Hospital, Fujian Branch of Shanghai Children’s Medical Center Affiliated to Shanghai Jiaotong University School of Medicine, Fuzhou, China
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21
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Contreras Yametti GP, Robbins G, Chowdhury A, Narang S, Ostrow TH, Kilberg H, Greenberg J, Kramer L, Raetz E, Tsirigos A, Evensen NA, Carroll WL. SETD2 mutations do not contribute to clonal fitness in response to chemotherapy in childhood B cell acute lymphoblastic leukemia. Leuk Lymphoma 2024; 65:78-90. [PMID: 37874744 DOI: 10.1080/10428194.2023.2273752] [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: 06/19/2023] [Accepted: 10/14/2023] [Indexed: 10/26/2023]
Abstract
Mutations in genes encoding epigenetic regulators are commonly observed at relapse in B cell acute lymphoblastic leukemia (B-ALL). Loss-of-function mutations in SETD2, an H3K36 methyltransferase, have been observed in B-ALL and other cancers. Previous studies on mutated SETD2 in solid tumors and acute myelogenous leukemia support a role in promoting resistance to DNA damaging agents. We did not observe chemoresistance, an impaired DNA damage response, nor increased mutation frequency in response to thiopurines using CRISPR-mediated knockout in wild-type B-ALL cell lines. Likewise, restoration of SETD2 in cell lines with hemizygous mutations did not increase sensitivity. SETD2 mutations affected the chromatin landscape and transcriptional output that was unique to each cell line. Collectively our data does not support a role for SETD2 mutations in driving clonal evolution and relapse in B-ALL, which is consistent with the lack of enrichment of SETD2 mutations at relapse in most studies.
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Affiliation(s)
- Gloria P Contreras Yametti
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Gabriel Robbins
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Ashfiyah Chowdhury
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Sonali Narang
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Talia H Ostrow
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Harrison Kilberg
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Joshua Greenberg
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Lindsay Kramer
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Elizabeth Raetz
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Aristotelis Tsirigos
- Departments of Pediatrics and Pathology, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Nikki A Evensen
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - William L Carroll
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
- Department of Pathology, NYU Langone Health, New York, NY, USA
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22
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Zimmerman JAO, Fang M, Pufall MA. PI3Kδ Inhibition Potentiates Glucocorticoids in B-lymphoblastic Leukemia by Decreasing Receptor Phosphorylation and Enhancing Gene Regulation. Cancers (Basel) 2023; 16:143. [PMID: 38201570 PMCID: PMC10778422 DOI: 10.3390/cancers16010143] [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: 11/17/2023] [Revised: 12/14/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
Glucocorticoids are the cornerstone of B-lymphoblastic leukemia (B-ALL) therapy. Because response to glucocorticoids alone predicts overall outcomes for B-ALL, enhancing glucocorticoid potency should improve treatment. We previously showed that inhibition of the lymphoid-restricted PI3Kδ with idelalisib enhances glucocorticoid activity in B-ALL cells. Here, we show that idelalisib enhances glucocorticoid potency in 90% of primary B-ALL specimens and is most pronounced at sub-saturating doses of glucocorticoids near the EC50. Potentiation is associated with enhanced regulation of all glucocorticoid-regulated genes, including genes that drive B-ALL cell death. Idelalisib reduces phosphorylation of the glucocorticoid receptor (GR) at PI3Kδ/MAPK1 (ERK2) targets S203 and S226. Ablation of these phospho-acceptor sites enhances sensitivity to glucocorticoids with ablation of S226 in particular reducing synergy. We also show that phosphorylation of S226 reduces the affinity of GR for DNA in vitro. We propose that PI3Kδ inhibition improves glucocorticoid efficacy in B-ALL in part by decreasing GR phosphorylation, increasing DNA binding affinity, and enhancing downstream gene regulation. This mechanism and the response of patient specimens suggest that idelalisib will benefit most patients with B-ALL, but particularly patients with less responsive, including high-risk, disease. This combination is also promising for the development of less toxic glucocorticoid-sparing therapies.
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Affiliation(s)
- Jessica A. O. Zimmerman
- Division of Pediatric Hematology/Oncology, Stead Family Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA;
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52242, USA;
| | - Mimi Fang
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52242, USA;
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Miles A. Pufall
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52242, USA;
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
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23
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Barrios-Palacios D, Organista-Nava J, Balandrán JC, Alarcón-Romero LDC, Zubillaga-Guerrero MI, Illades-Aguiar B, Rivas-Alarcón AA, Diaz-Lucas JJ, Gómez-Gómez Y, Leyva-Vázquez MA. The Role of miRNAs in Childhood Acute Lymphoblastic Leukemia Relapse and the Associated Molecular Mechanisms. Int J Mol Sci 2023; 25:119. [PMID: 38203290 PMCID: PMC10779195 DOI: 10.3390/ijms25010119] [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: 11/28/2023] [Revised: 12/15/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common cancer in children worldwide. Although ALL patients' overall survival rates in wealthy countries currently surpass 80%, 15-20% of patients still experience relapse. The underlying mechanisms of relapse are still not fully understood, and little progress has been made in treating refractory or relapsed disease. Disease relapse and treatment failure are common causes of leukemia-related death. In ALL relapse, several gene signatures have been identified, but it is also important to study miRNAs involved in ALL relapse in an effort to avoid relapse and to achieve better survival rates since miRNAs regulate target genes that participate in signaling pathways involved in relapse, such as those related to drug resistance, survival signals, and antiapoptotic mechanisms. Several miRNAs, such as miR-24, miR-27a, miR-99/100, miR-124, miR-1225b, miR-128b, miR-142-3p, miR-155 and miR-335-3p, are valuable biomarkers for prognosis and treatment response in ALL patients. Thus, this review aimed to analyze the primary miRNAs involved in pediatric ALL relapse and explore the underlying molecular mechanisms in an effort to identify miRNAs that may be potential candidates for anti-ALL therapy soon.
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Affiliation(s)
- Dalia Barrios-Palacios
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo 39090, Guerrero, Mexico; (D.B.-P.); (J.O.-N.); (B.I.-A.); (A.A.R.-A.); (J.J.D.-L.)
| | - Jorge Organista-Nava
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo 39090, Guerrero, Mexico; (D.B.-P.); (J.O.-N.); (B.I.-A.); (A.A.R.-A.); (J.J.D.-L.)
| | - Juan Carlos Balandrán
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA;
| | - Luz del Carmen Alarcón-Romero
- Laboratorio de Citopatología, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo 39090, Guerrero, Mexico; (L.d.C.A.-R.); (M.I.Z.-G.)
| | - Ma Isabel Zubillaga-Guerrero
- Laboratorio de Citopatología, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo 39090, Guerrero, Mexico; (L.d.C.A.-R.); (M.I.Z.-G.)
| | - Berenice Illades-Aguiar
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo 39090, Guerrero, Mexico; (D.B.-P.); (J.O.-N.); (B.I.-A.); (A.A.R.-A.); (J.J.D.-L.)
| | - Alinne Ayulieth Rivas-Alarcón
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo 39090, Guerrero, Mexico; (D.B.-P.); (J.O.-N.); (B.I.-A.); (A.A.R.-A.); (J.J.D.-L.)
| | - Jessica Julieth Diaz-Lucas
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo 39090, Guerrero, Mexico; (D.B.-P.); (J.O.-N.); (B.I.-A.); (A.A.R.-A.); (J.J.D.-L.)
| | - Yazmín Gómez-Gómez
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo 39090, Guerrero, Mexico; (D.B.-P.); (J.O.-N.); (B.I.-A.); (A.A.R.-A.); (J.J.D.-L.)
| | - Marco Antonio Leyva-Vázquez
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo 39090, Guerrero, Mexico; (D.B.-P.); (J.O.-N.); (B.I.-A.); (A.A.R.-A.); (J.J.D.-L.)
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24
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Antić Ž, Lentes J, Bergmann AK. Cytogenetics and genomics in pediatric acute lymphoblastic leukaemia. Best Pract Res Clin Haematol 2023; 36:101511. [PMID: 38092485 DOI: 10.1016/j.beha.2023.101511] [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: 03/22/2023] [Revised: 07/24/2023] [Accepted: 08/15/2023] [Indexed: 12/18/2023]
Abstract
The last five decades have witnessed significant improvement in diagnostics, treatment and management of children with acute lymphoblastic leukaemia (ALL). These advancements have become possible through progress in our understanding of the genetic and biological background of ALL, resulting in the introduction of risk-adapted treatment and novel therapeutic targets, e.g., tyrosine kinase inhibitors for BCR::ABL1-positive ALL. Further advances in the taxonomy of ALL and the discovery of new genetic biomarkers and therapeutic targets, as well as the introduction of targeted and immunotherapies into the frontline treatment protocols, may improve management and outcome of children with ALL. In this review we describe the current developments in the (cyto)genetic diagnostics and management of children with ALL, and provide an overview of the most important advances in the genetic classification of ALL. Furthermore, we discuss perspectives resulting from the development of new techniques, including artificial intelligence (AI).
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Affiliation(s)
- Željko Antić
- Department of Human Genetics, Hannover Medical School (MHH), Hannover, Germany
| | - Jana Lentes
- Department of Human Genetics, Hannover Medical School (MHH), Hannover, Germany
| | - Anke K Bergmann
- Department of Human Genetics, Hannover Medical School (MHH), Hannover, Germany.
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25
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van der Krift F, Zijlmans DW, Shukla R, Javed A, Koukos PI, Schwarz LLE, Timmermans-Sprang EP, Maas PE, Gahtory D, van den Nieuwboer M, Mol JA, Strous GJ, Bonvin AM, van der Stelt M, Veldhuizen EJ, Weingarth M, Vermeulen M, Klumperman J, Maurice MM. A novel antifolate suppresses growth of FPGS-deficient cells and overcomes methotrexate resistance. Life Sci Alliance 2023; 6:e202302058. [PMID: 37591722 PMCID: PMC10435995 DOI: 10.26508/lsa.202302058] [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: 03/24/2023] [Revised: 08/07/2023] [Accepted: 08/07/2023] [Indexed: 08/19/2023] Open
Abstract
Cancer cells make extensive use of the folate cycle to sustain increased anabolic metabolism. Multiple chemotherapeutic drugs interfere with the folate cycle, including methotrexate and 5-fluorouracil that are commonly applied for the treatment of leukemia and colorectal cancer (CRC), respectively. Despite high success rates, therapy-induced resistance causes relapse at later disease stages. Depletion of folylpolyglutamate synthetase (FPGS), which normally promotes intracellular accumulation and activity of natural folates and methotrexate, is linked to methotrexate and 5-fluorouracil resistance and its association with relapse illustrates the need for improved intervention strategies. Here, we describe a novel antifolate (C1) that, like methotrexate, potently inhibits dihydrofolate reductase and downstream one-carbon metabolism. Contrary to methotrexate, C1 displays optimal efficacy in FPGS-deficient contexts, due to decreased competition with intracellular folates for interaction with dihydrofolate reductase. We show that FPGS-deficient patient-derived CRC organoids display enhanced sensitivity to C1, whereas FPGS-high CRC organoids are more sensitive to methotrexate. Our results argue that polyglutamylation-independent antifolates can be applied to exert selective pressure on FPGS-deficient cells during chemotherapy, using a vulnerability created by polyglutamylation deficiency.
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Affiliation(s)
- Felix van der Krift
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Dick W Zijlmans
- Department of Molecular Biology and Oncode Institute, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Rhythm Shukla
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Ali Javed
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
- Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - Panagiotis I Koukos
- Computational Structural Biology, Bijvoet Centre for Biomolecular Research, Faculty of Science, Department of Chemistry, Utrecht University, Utrecht, The Netherlands
| | - Laura LE Schwarz
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Peter Em Maas
- Specs Compound Handling B.V., Zoetermeer, The Netherlands
| | | | | | - Jan A Mol
- Department of Clinical Sciences of Companion Animals, Utrecht University, Utrecht, The Netherlands
| | - Ger J Strous
- Center for Molecular Medicine, Cell Biology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Alexandre Mjj Bonvin
- Computational Structural Biology, Bijvoet Centre for Biomolecular Research, Faculty of Science, Department of Chemistry, Utrecht University, Utrecht, The Netherlands
| | - Mario van der Stelt
- Department of Molecular Physiology and Oncode Institute, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Edwin Ja Veldhuizen
- Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - Markus Weingarth
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology and Oncode Institute, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Judith Klumperman
- Center for Molecular Medicine, Cell Biology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Madelon M Maurice
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
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26
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Wang H, Sun H, Liang B, Zhang F, Yang F, Cui B, Ding L, Wang X, Wang R, Cai J, Tang Y, Rao J, Hu W, Zhao S, Wu W, Chen X, Wu K, Lai J, Xie Y, Li B, Tang J, Shen S, Liu Y. Chromatin accessibility landscape of relapsed pediatric B-lineage acute lymphoblastic leukemia. Nat Commun 2023; 14:6792. [PMID: 37880218 PMCID: PMC10600232 DOI: 10.1038/s41467-023-42565-z] [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: 03/03/2023] [Accepted: 10/13/2023] [Indexed: 10/27/2023] Open
Abstract
For around half of the pediatric B-lineage acute lymphoblastic leukemia (B-ALL) patients, the molecular mechanism of relapse remains unclear. To fill this gap in knowledge, here we characterize the chromatin accessibility landscape in pediatric relapsed B-ALL. We observe rewired accessible chromatin regions (ACRs) associated with transcription dysregulation in leukemia cells as compared with normal B-cell progenitors. We show that over a quarter of the ACRs in B-ALL are in quiescent regions with high heterogeneity among B-ALLs. We identify subtype-specific and allele-imbalanced chromatin accessibility by integrating multi-omics data. By characterizing the differential ACRs between diagnosis and relapse in B-ALL, we identify alterations in chromatin accessibility during drug treatment. Further analysis of ACRs associated with relapse free survival leads to the identification of a subgroup of B-ALL which show early relapse. These data provide an advanced and integrative portrait of the importance of chromatin accessibility alterations in tumorigenesis and drug responses.
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Affiliation(s)
- Han Wang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Huiying Sun
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Bilin Liang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fang Zhang
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fan Yang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Bowen Cui
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lixia Ding
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiang Wang
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ronghua Wang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jiaoyang Cai
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yanjing Tang
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jianan Rao
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wenting Hu
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shuang Zhao
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wenyan Wu
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoxiao Chen
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Kefei Wu
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Junchen Lai
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yangyang Xie
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Benshang Li
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jingyan Tang
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shuhong Shen
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Fujian Children's Hospital, Fujian Branch of Shanghai Children's Medical Center Affiliated to Shanghai Jiao Tong University School of Medicine, Fuzhou, China.
| | - Yu Liu
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Fujian Children's Hospital, Fujian Branch of Shanghai Children's Medical Center Affiliated to Shanghai Jiao Tong University School of Medicine, Fuzhou, China.
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27
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Caserta C, Nucera S, Barcella M, Fazio G, Naldini MM, Pagani R, Pavesi F, Desantis G, Zonari E, D'Angiò M, Capasso P, Lombardo A, Merelli I, Spinelli O, Rambaldi A, Ciceri F, Silvestri D, Valsecchi MG, Biondi A, Cazzaniga G, Gentner B. miR-126 identifies a quiescent and chemo-resistant human B-ALL cell subset that correlates with minimal residual disease. Leukemia 2023; 37:1994-2005. [PMID: 37640845 DOI: 10.1038/s41375-023-02009-5] [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: 03/14/2023] [Revised: 08/03/2023] [Accepted: 08/17/2023] [Indexed: 08/31/2023]
Abstract
Complete elimination of B-cell acute lymphoblastic leukemia (B-ALL) by a risk-adapted primary treatment approach remains a clinical key objective, which fails in up to a third of patients. Recent evidence has implicated subpopulations of B-ALL cells with stem-like features in disease persistence. We hypothesized that microRNA-126, a core regulator of hematopoietic and leukemic stem cells, may resolve intratumor heterogeneity in B-ALL and uncover therapy-resistant subpopulations. We exploited patient-derived xenograft (PDX) models with B-ALL cells transduced with a miR-126 reporter allowing the prospective isolation of miR-126(high) cells for their functional and transcriptional characterization. Discrete miR-126(high) populations, often characterized by MIR126 locus demethylation, were identified in 8/9 PDX models and showed increased repopulation potential, in vivo chemotherapy resistance and hallmarks of quiescence, inflammation and stress-response pathway activation. Cells with a miR-126(high) transcriptional profile were identified as distinct disease subpopulations by single-cell RNA sequencing in diagnosis samples from adult and pediatric B-ALL. Expression of miR-126 and locus methylation were tested in several pediatric and adult B-ALL cohorts, which received standardized treatment. High microRNA-126 levels and locus demethylation at diagnosis associate with suboptimal response to induction chemotherapy (MRD > 0.05% at day +33 or MRD+ at day +78).
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Affiliation(s)
- Carolina Caserta
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Silvia Nucera
- Tettamanti Center, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
- School of Medicine and Surgery, University of Milano Bicocca, Monza, Italy
| | - Matteo Barcella
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, Italy
- National Research Council, Institute for Biomedical Technologies, Segrate, Italy
| | - Grazia Fazio
- Tettamanti Center, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Matteo Maria Naldini
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Riccardo Pagani
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Francesca Pavesi
- Hematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Hospital, Milan, Italy
| | - Giacomo Desantis
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Erika Zonari
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Mariella D'Angiò
- Tettamanti Center, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Paola Capasso
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Angelo Lombardo
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Ivan Merelli
- National Research Council, Institute for Biomedical Technologies, Segrate, Italy
| | - Orietta Spinelli
- Hematology and Bone Marrow Transplant Unit, Ospedale Papa Giovanni XXIII, Bergamo, Italy
| | - Alessandro Rambaldi
- Hematology and Bone Marrow Transplant Unit, Ospedale Papa Giovanni XXIII, Bergamo, Italy
| | - Fabio Ciceri
- Vita-Salute San Raffaele University, Milan, Italy
- Hematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Hospital, Milan, Italy
| | - Daniela Silvestri
- Tettamanti Center, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Maria Grazia Valsecchi
- Bicocca Bioinformatics, Biostatistics and Bioimaging Centre, Department of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Andrea Biondi
- Tettamanti Center, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
- School of Medicine and Surgery, University of Milano Bicocca, Monza, Italy
- Pediatrics, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italia
| | - Giovanni Cazzaniga
- Tettamanti Center, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
- Genetics, School of Medicine and Surgery, University of Milano Bicocca, Monza, Italy
| | - Bernhard Gentner
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, Italy.
- Hematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Hospital, Milan, Italy.
- Ludwig Institute for Cancer Research and Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland.
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28
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Zimmerman JA, Fang M, Pufall MA. PI3Kδ inhibition potentiates glucocorticoids in B-lymphoblastic leukemia by decreasing receptor phosphorylation and enhancing gene regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.10.527869. [PMID: 36798391 PMCID: PMC9934697 DOI: 10.1101/2023.02.10.527869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
Abstract
Glucocorticoids, including dexamethasone and prednisone, are the cornerstone of B-lymphoblastic leukemia (B-ALL) therapy. Because response to glucocorticoids alone predicts overall outcomes for B-ALL, enhancing glucocorticoid potency is a route to improving outcomes. However, systematic toxicities prevent the use of higher dose and more potent glucocorticoids. We therefore took a functional genomic approach to identify targets to enhance glucocorticoid activity specifically in B-ALL cells. Here we show that inhibition of the lymphoid-restricted PI3Kδ, signaling through the RAS/MAPK pathway, enhances both prednisone and dexamethasone activity in almost all ex vivo B-ALL specimens tested. This potentiation is most synergistic at sub-saturating doses of glucocorticoids, approaching the EC50. Potentiation correlates with global enhancement of glucocorticoid-induced gene regulation, including regulation of effector genes that drive B-ALL cell death. Idelalisib reduces phosphorylation of the glucocorticoid receptor (GR) at MAPK1/ERK2 targets S203 and S226, and ablation of these phospho-acceptor sites enhances glucocorticoid potency. We further show that phosphorylation of S226 reduces the affinity of GR for DNA in vitro, which impairs DNA binding. We therefore propose that PI3Kδ inhibition improves glucocorticoid efficacy in B-ALL in part by decreasing GR phosphorylation, increasing DNA binding affinity, and enhancing downstream gene regulation. The overall enhancement of GR function suggests that idelalisib will provide benefit to most patients with B-ALL by improving outcomes for patients whose disease is less responsive to glucocorticoid-based therapy, including high-risk disease, and allowing less toxic glucocorticoid-sparing strategies for patients with standard-risk disease.
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Affiliation(s)
- Jessica A.O. Zimmerman
- Division of Pediatric Hematology/Oncology, Stead Family Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA
| | - Mimi Fang
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Miles A. Pufall
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
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29
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Wu X, Li Z, Wang ZQ, Xu X. The neurological and non-neurological roles of the primary microcephaly-associated protein ASPM. Front Neurosci 2023; 17:1242448. [PMID: 37599996 PMCID: PMC10436222 DOI: 10.3389/fnins.2023.1242448] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 07/24/2023] [Indexed: 08/22/2023] Open
Abstract
Primary microcephaly (MCPH), is a neurological disorder characterized by small brain size that results in numerous developmental problems, including intellectual disability, motor and speech delays, and seizures. Hitherto, over 30 MCPH causing genes (MCPHs) have been identified. Among these MCPHs, MCPH5, which encodes abnormal spindle-like microcephaly-associated protein (ASPM), is the most frequently mutated gene. ASPM regulates mitotic events, cell proliferation, replication stress response, DNA repair, and tumorigenesis. Moreover, using a data mining approach, we have confirmed that high levels of expression of ASPM correlate with poor prognosis in several types of tumors. Here, we summarize the neurological and non-neurological functions of ASPM and provide insight into its implications for the diagnosis and treatment of MCPH and cancer.
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Affiliation(s)
- Xingxuan Wu
- Guangdong Key Laboratory for Genome Stability and Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, Guangdong, China
- Shenzhen University-Friedrich Schiller Universität Jena Joint PhD Program in Biomedical Sciences, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
- Laboratory of Genome Stability, Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany
| | - Zheng Li
- Guangdong Key Laboratory for Genome Stability and Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, Guangdong, China
| | - Zhao-Qi Wang
- Shenzhen University-Friedrich Schiller Universität Jena Joint PhD Program in Biomedical Sciences, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
- Laboratory of Genome Stability, Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany
| | - Xingzhi Xu
- Guangdong Key Laboratory for Genome Stability and Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, Guangdong, China
- Shenzhen University-Friedrich Schiller Universität Jena Joint PhD Program in Biomedical Sciences, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
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30
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Coorens THH, Collord G, Treger TD, Adams S, Mitchell E, Newman B, Getz G, Godfrey AL, Bartram J, Behjati S. Clonal origin of KMT2A wild-type lineage-switch leukemia following CAR-T cell and blinatumomab therapy. NATURE CANCER 2023; 4:1095-1101. [PMID: 37474833 PMCID: PMC10447231 DOI: 10.1038/s43018-023-00604-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 06/22/2023] [Indexed: 07/22/2023]
Abstract
Children with acute lymphoblastic leukemia (ALL) undergoing anti-CD19 therapy occasionally develop acute myeloid leukemia (AML). The clonal origin of such lineage-switch leukemias1-4 remains unresolved. Here, we reconstructed the phylogeny of multiple leukemias in a girl who, following multiply relapsed ALL, received anti-CD19 cellular and antibody treatment and subsequently developed AML. Whole genome sequencing unambiguously revealed the AML derived from the initial ALL, with distinct driver mutations that were detectable before emergence. Extensive prior diversification and subsequent clonal selection underpins this fatal lineage switch. Genomic monitoring of primary leukemias and recurrences may predict therapy resistance, especially regarding anti-CD19 treatment.
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Affiliation(s)
| | - Grace Collord
- Great Ormond Street Hospital for Children, London, UK
| | - Taryn D Treger
- Wellcome Sanger Institute, Hinxton, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Stuart Adams
- Great Ormond Street Hospital for Children, London, UK
| | - Emily Mitchell
- Wellcome Sanger Institute, Hinxton, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Barbara Newman
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Anna L Godfrey
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Jack Bartram
- Great Ormond Street Hospital for Children, London, UK
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Department of Paediatrics, University of Cambridge, Cambridge, UK.
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31
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Donker HC, Cuppens K, Froyen G, Groen HJM, Hiltermann TJN, Maes B, Schuuring E, Volders PJ, Lunter GA, van Es B. Reliability of panel-based mutational signatures for immune-checkpoint-inhibition efficacy prediction in non-small cell lung cancer. Lung Cancer 2023; 182:107286. [PMID: 37421934 DOI: 10.1016/j.lungcan.2023.107286] [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: 05/09/2023] [Revised: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 07/10/2023]
Abstract
OBJECTIVES Mutational signatures (MS) are gaining traction for deriving therapeutic insights for immune checkpoint inhibition (ICI). We asked if MS attributions from comprehensive targeted sequencing assays are reliable enough for predicting ICI efficacy in non-small cell lung cancer (NSCLC). METHODS Somatic mutations of m = 126 patients were assayed using panel-based sequencing of 523 cancer-related genes. In silico simulations of MS attributions for various panels were performed on a separate dataset of m = 101 whole genome sequenced patients. Non-synonymous mutations were deconvoluted using COSMIC v3.3 signatures and used to test a previously published machine learning classifier. RESULTS The ICI efficacy predictor performed poorly with an accuracy of 0.51-0.09+0.09, average precision of 0.52-0.11+0.11, and an area under the receiver operating characteristic curve of 0.50-0.09+0.10. Theoretical arguments, experimental data, and in silico simulations pointed to false negative rates (FNR) related to panel size. A secondary effect was observed, where deconvolution of small ensembles of point mutations lead to reconstruction errors and misattributions. CONCLUSION MS attributions from current targeted panel sequencing are not reliable enough to predict ICI efficacy. We suggest that, for downstream classification tasks in NSCLC, signature attributions be based on whole exome or genome sequencing instead.
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Affiliation(s)
- H C Donker
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; Global Computational Biology & Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany.
| | - K Cuppens
- Department of Pulmonology and Thoracic Oncology, Jessa Hospital, Hasselt, Belgium; Department of Thoracic Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Faculty of Medicine and Life Sciences - LCRC, Hasselt University, Diepenbeek, Belgium.
| | - G Froyen
- Faculty of Medicine and Life Sciences - LCRC, Hasselt University, Diepenbeek, Belgium; Laboratory of Molecular Diagnostics, Dept Clinical Biology, Jessa Hospital, Hasselt, Belgium
| | - H J M Groen
- Department of Pulmonary Diseases, University of Groningen and University Medical Center Groningen, the Netherlands.
| | - T J N Hiltermann
- Department of Pulmonary Diseases, University of Groningen and University Medical Center Groningen, the Netherlands.
| | - B Maes
- Faculty of Medicine and Life Sciences - LCRC, Hasselt University, Diepenbeek, Belgium; Laboratory of Molecular Diagnostics, Dept Clinical Biology, Jessa Hospital, Hasselt, Belgium.
| | - E Schuuring
- Department of Pathology, University of Groningen and University Medical Center Groningen, the Netherlands.
| | - P-J Volders
- Laboratory of Molecular Diagnostics, Dept Clinical Biology, Jessa Hospital, Hasselt, Belgium.
| | - G A Lunter
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, UK.
| | - B van Es
- Central Diagnostic Laboratory, University Medical Centre Utrecht, Utrecht University, Heidelberglaan 100, 3508 GA Utrecht, the Netherlands; MedxAI, Theophile de Bockstraat 77-1, 1058VA Amsterdam, the Netherlands.
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32
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Levinson AL, Tjoa K, Huang B, Meyer LK, Kim MO, Brady SW, Zhang J, Shannon K, Wandler AM. Opposing effects of KDM6A and JDP2 on glucocorticoid sensitivity in T-ALL. Blood Adv 2023; 7:3479-3484. [PMID: 36897249 PMCID: PMC10362263 DOI: 10.1182/bloodadvances.2021006881] [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: 12/21/2021] [Revised: 01/27/2023] [Accepted: 02/21/2023] [Indexed: 03/11/2023] Open
Abstract
Glucocorticoids (GCs) are the cornerstone of acute lymphoblastic leukemia (ALL) therapy. Although mutations in NR3C1, which encodes the GC receptor (GR), and other genes involved in GC signaling occur at relapse, additional mechanisms of adaptive GC resistance are uncertain. We transplanted and treated 10 primary mouse T-lineage acute lymphoblastic leukemias (T-ALLs) initiated by retroviral insertional mutagenesis with GC dexamethasone (DEX). Multiple distinct relapsed clones from 1 such leukemia (T-ALL 8633) exhibited discrete retroviral integrations that upregulated Jdp2 expression. This leukemia harbored a Kdm6a mutation. In the human T-ALL cell line CCRF-CEM, enforced JDP2 overexpression conferred GC resistance, whereas KDM6A inactivation unexpectedly enhanced GC sensitivity. In the context of KDM6A knockout, JDP2 overexpression induced profound GC resistance, counteracting the sensitization conferred by KDM6A loss. These resistant "double mutant" cells with combined KDM6A loss and JDP2 overexpression exhibited decreased NR3C1 mRNA and GR protein upregulation upon DEX exposure. Analysis of paired samples from 2 patients with KDM6A-mutant T-ALL in a relapsed pediatric ALL cohort revealed a somatic NR3C1 mutation at relapse in 1 patient and a markedly elevated JDP2 expression in the other. Together, these data implicate JDP2 overexpression as a mechanism of adaptive GC resistance in T-ALL, which functionally interacts with KDM6A inactivation.
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Affiliation(s)
- Anya L. Levinson
- Department of Pediatrics, University of California, San Francisco, CA
| | - Karensa Tjoa
- Department of Pediatrics, University of California, San Francisco, CA
| | - Benjamin Huang
- Department of Pediatrics, University of California, San Francisco, CA
| | - Lauren K. Meyer
- Department of Pediatrics, University of California, San Francisco, CA
| | - Mi-Ok Kim
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA
| | - Samuel W. Brady
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Kevin Shannon
- Department of Pediatrics, University of California, San Francisco, CA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA
| | - Anica M. Wandler
- Department of Pediatrics, University of California, San Francisco, CA
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33
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Li Z, Chang TC, Junco JJ, Devidas M, Li Y, Yang W, Huang X, Hedges DJ, Cheng Z, Shago M, Carroll AJ, Heerema NA, Gastier-Foster J, Wood BL, Borowitz MJ, Sanclemente L, Raetz EA, Hunger SP, Feingold E, Rosser TC, Sherman SL, Loh ML, Mullighan CG, Yu J, Wu G, Lupo PJ, Rabin KR, Yang JJ. Genomic landscape of Down syndrome-associated acute lymphoblastic leukemia. Blood 2023; 142:172-184. [PMID: 37001051 PMCID: PMC10352600 DOI: 10.1182/blood.2023019765] [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: 01/18/2023] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 04/03/2023] Open
Abstract
Trisomy 21, the genetic cause of Down syndrome (DS), is the most common congenital chromosomal anomaly. It is associated with a 20-fold increased risk of acute lymphoblastic leukemia (ALL) during childhood and results in distinctive leukemia biology. To comprehensively define the genomic landscape of DS-ALL, we performed whole-genome sequencing and whole-transcriptome sequencing (RNA-Seq) on 295 cases. Our integrated genomic analyses identified 15 molecular subtypes of DS-ALL, with marked enrichment of CRLF2-r, IGH::IGF2BP1, and C/EBP altered (C/EBPalt) subtypes compared with 2257 non-DS-ALL cases. We observed abnormal activation of the CEBPD, CEBPA, and CEBPE genes in 10.5% of DS-ALL cases via a variety of genomic mechanisms, including chromosomal rearrangements and noncoding mutations leading to enhancer hijacking. A total of 42.3% of C/EBP-activated DS-ALL also have concomitant FLT3 point mutations or insertions/deletions, compared with 4.1% in other subtypes. CEBPD overexpression enhanced the differentiation of mouse hematopoietic progenitor cells into pro-B cells in vitro, particularly in a DS genetic background. Notably, recombination-activating gene-mediated somatic genomic abnormalities were common in DS-ALL, accounting for a median of 27.5% of structural alterations, compared with 7.7% in non-DS-ALL. Unsupervised hierarchical clustering analyses of CRLF2-rearranged DS-ALL identified substantial heterogeneity within this group, with the BCR::ABL1-like subset linked to an inferior event-free survival, even after adjusting for known clinical risk factors. These results provide important insights into the biology of DS-ALL and point to opportunities for targeted therapy and treatment individualization.
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Affiliation(s)
- Zhenhua Li
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN
| | - Ti-Cheng Chang
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN
| | - Jacob J. Junco
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - Meenakshi Devidas
- Global Pediatric Medicine, St. Jude Children’s Research Hospital, Memphis, TN
| | - Yizhen Li
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN
| | - Wenjian Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN
| | - Xin Huang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Dale J. Hedges
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN
| | - Zhongshan Cheng
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN
| | - Mary Shago
- Department of Pathobiology and Laboratory Medicine, University of Toronto, Toronto, ON, Canada
| | - Andrew J. Carroll
- Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL
| | - Nyla A. Heerema
- Department of Pathology, The Ohio State University, Columbus, OH
| | - Julie Gastier-Foster
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX
| | - Brent L. Wood
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, University of Southern California, Los Angeles, CA
| | | | | | - Elizabeth A. Raetz
- Department of Pediatrics and Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY
| | - Stephen P. Hunger
- Department of Pediatrics and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA
- The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Eleanor Feingold
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA
| | | | | | - Mignon L. Loh
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Department of Pediatrics, Seattle Children’s Hospital, University of Washington, Seattle, WA
| | | | - Jiyang Yu
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Gang Wu
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Philip J. Lupo
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - Karen R. Rabin
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - Jun J. Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
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34
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Borin C, Pieters T, Serafin V, Ntziachristos P. Emerging Epigenetic and Posttranslational Mechanisms Controlling Resistance to Glucocorticoids in Acute Lymphoblastic Leukemia. Hemasphere 2023; 7:e916. [PMID: 37359189 PMCID: PMC10289758 DOI: 10.1097/hs9.0000000000000916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/16/2023] [Indexed: 06/28/2023] Open
Abstract
Glucocorticoids are extensively used for the treatment of acute lymphoblastic leukemia as they pressure cancer cells to undergo apoptosis. Nevertheless, glucocorticoid partners, modifications, and mechanisms of action are hitherto poorly characterized. This hampers our understanding of therapy resistance, frequently occurring in leukemia despite the current therapeutic combinations using glucocorticoids in acute lymphoblastic leukemia. In this review, we initially cover the traditional view of glucocorticoid resistance and ways of targeting this resistance. We discuss recent progress in our understanding of chromatin and posttranslational properties of the glucocorticoid receptor that might be proven beneficial in our efforts to understand and target therapy resistance. We discuss emerging roles of pathways and proteins such as the lymphocyte-specific kinase that antagonizes glucocorticoid receptor activation and nuclear translocation. In addition, we provide an overview of ongoing therapeutic approaches that sensitize cells to glucocorticoids including small molecule inhibitors and proteolysis-targeting chimeras.
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Affiliation(s)
- Cristina Borin
- Department of Biomolecular Medicine, Ghent University, Belgium
- Center for Medical Genetics, Ghent University and University Hospital, Belgium
- Cancer Research Institute Ghent (CRIG), Belgium
| | - Tim Pieters
- Department of Biomolecular Medicine, Ghent University, Belgium
- Center for Medical Genetics, Ghent University and University Hospital, Belgium
- Cancer Research Institute Ghent (CRIG), Belgium
| | - Valentina Serafin
- Department of Surgery Oncology and Gastroenterology, Oncology and Immunology Section, University of Padova, Italy
| | - Panagiotis Ntziachristos
- Department of Biomolecular Medicine, Ghent University, Belgium
- Center for Medical Genetics, Ghent University and University Hospital, Belgium
- Cancer Research Institute Ghent (CRIG), Belgium
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35
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Sarno J, Domizi P, Liu Y, Merchant M, Pedersen CB, Jedoui D, Jager A, Nolan GP, Gaipa G, Bendall SC, Bava FA, Davis KL. Dasatinib overcomes glucocorticoid resistance in B-cell acute lymphoblastic leukemia. Nat Commun 2023; 14:2935. [PMID: 37217509 DOI: 10.1038/s41467-023-38456-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 04/28/2023] [Indexed: 05/24/2023] Open
Abstract
Resistance to glucocorticoids (GC) is associated with an increased risk of relapse in B-cell progenitor acute lymphoblastic leukemia (BCP-ALL). Performing transcriptomic and single-cell proteomic studies in healthy B-cell progenitors, we herein identify coordination between the glucocorticoid receptor pathway with B-cell developmental pathways. Healthy pro-B cells most highly express the glucocorticoid receptor, and this developmental expression is conserved in primary BCP-ALL cells from patients at diagnosis and relapse. In-vitro and in vivo glucocorticoid treatment of primary BCP-ALL cells demonstrate that the interplay between B-cell development and the glucocorticoid pathways is crucial for GC resistance in leukemic cells. Gene set enrichment analysis in BCP-ALL cell lines surviving GC treatment show enrichment of B cell receptor signaling pathways. In addition, primary BCP-ALL cells surviving GC treatment in vitro and in vivo demonstrate a late pre-B cell phenotype with activation of PI3K/mTOR and CREB signaling. Dasatinib, a multi-kinase inhibitor, most effectively targets this active signaling in GC-resistant cells, and when combined with glucocorticoids, results in increased cell death in vitro and decreased leukemic burden and prolonged survival in an in vivo xenograft model. Targeting the active signaling through the addition of dasatinib may represent a therapeutic approach to overcome GC resistance in BCP-ALL.
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Affiliation(s)
- Jolanda Sarno
- Hematology, Oncology, Stem Cell Transplant, and Regenerative Medicine, Department of Pediatrics, Stanford University, Stanford, CA, USA.
| | - Pablo Domizi
- Hematology, Oncology, Stem Cell Transplant, and Regenerative Medicine, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Yuxuan Liu
- Hematology, Oncology, Stem Cell Transplant, and Regenerative Medicine, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Milton Merchant
- Hematology, Oncology, Stem Cell Transplant, and Regenerative Medicine, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Christina Bligaard Pedersen
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Dorra Jedoui
- Hematology, Oncology, Stem Cell Transplant, and Regenerative Medicine, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Astraea Jager
- Hematology, Oncology, Stem Cell Transplant, and Regenerative Medicine, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Giuseppe Gaipa
- M. Tettamanti Research Center, Fondazione IRCCS San Gerardo dei Tintori, Monza, (MB), Italy
| | - Sean C Bendall
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Felice-Alessio Bava
- Baxter Laboratory, Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
- Institut national de la santé et de la recherche médicale (INSERM), Paris, France
| | - Kara L Davis
- Hematology, Oncology, Stem Cell Transplant, and Regenerative Medicine, Department of Pediatrics, Stanford University, Stanford, CA, USA.
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36
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Yoshida M, Nakabayashi K, Yang W, Sato‐Otsubo A, Tsujimoto S, Ogata‐Kawata H, Kawai T, Ishiwata K, Sakamoto M, Okamura K, Yoshida K, Shirai R, Osumi T, Kiyotani C, Shioda Y, Terashima K, Ishimaru S, Yuza Y, Takagi M, Arakawa Y, Imamura T, Hasegawa D, Inoue A, Yoshioka T, Ito S, Tomizawa D, Koh K, Matsumoto K, Kiyokawa N, Ogawa S, Manabe A, Niwa A, Hata K, Yang JJ, Kato M. Prevalence of pathogenic variants in cancer-predisposing genes in second cancer after childhood solid cancers. Cancer Med 2023; 12:11264-11273. [PMID: 37021926 PMCID: PMC10242325 DOI: 10.1002/cam4.5835] [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: 05/12/2022] [Revised: 02/17/2023] [Accepted: 03/11/2023] [Indexed: 04/07/2023] Open
Abstract
BACKGROUND Second malignant neoplasms (SMNs) are one of the most severe late complications after pediatric cancer treatment. However, the effect of genetic variation on SMNs remains unclear. In this study, we revealed germline genetic factors that contribute to the development of SMNs after treatment of pediatric solid tumors. METHODS We performed whole-exome sequencing in 14 pediatric patients with SMNs, including three brain tumors. RESULTS Our analysis revealed that five of 14 (35.7%) patients had pathogenic germline variants in cancer-predisposing genes (CPGs), which was significantly higher than in the control cohort (p < 0.01). The identified genes with variants were TP53 (n = 2), DICER1 (n = 1), PMS2 (n = 1), and PTCH1 (n = 1). In terms of the type of subsequent cancer, leukemia and multiple episodes of SMN had an exceptionally high rate of CPG pathogenic variants. None of the patients with germline variants had a family history of SMN development. Mutational signature analysis showed that platinum drugs contributed to the development of SMN in three cases, which suggests the role of platinum agents in SMN development. CONCLUSIONS We highlight that overlapping effects of genetic background and primary cancer treatment contribute to the development of second cancers after treatment of pediatric solid tumors. A comprehensive analysis of germline and tumor samples may be useful to predict the risk of secondary cancers.
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Affiliation(s)
- Masanori Yoshida
- Department of Pediatric Hematology and Oncology ResearchResearch Institute, National Center for Child Health and DevelopmentTokyoJapan
- Department of Pediatrics, Graduate School of MedicineYokohama City UniversityYokohamaJapan
| | - Kazuhiko Nakabayashi
- Department of Maternal‐Fetal BiologyResearch Institute, National Center for Child Health and DevelopmentTokyoJapan
| | - Wentao Yang
- Department of Pharmacy and Pharmaceutical SciencesSt. Jude Children's Research HospitalTennesseeMemphisUSA
| | - Aiko Sato‐Otsubo
- Department of Pediatric Hematology and Oncology ResearchResearch Institute, National Center for Child Health and DevelopmentTokyoJapan
- Department of Pediatrics, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Shin‐ichi Tsujimoto
- Department of Pediatric Hematology and Oncology ResearchResearch Institute, National Center for Child Health and DevelopmentTokyoJapan
- Department of Pediatrics, Graduate School of MedicineYokohama City UniversityYokohamaJapan
| | - Hiroko Ogata‐Kawata
- Department of Maternal‐Fetal BiologyResearch Institute, National Center for Child Health and DevelopmentTokyoJapan
| | - Tomoko Kawai
- Department of Maternal‐Fetal BiologyResearch Institute, National Center for Child Health and DevelopmentTokyoJapan
| | - Keisuke Ishiwata
- Department of Maternal‐Fetal BiologyResearch Institute, National Center for Child Health and DevelopmentTokyoJapan
| | - Mika Sakamoto
- Medical Genome CenterResearch Institute, National Center for Child Health and DevelopmentTokyoJapan
| | - Kohji Okamura
- Department of Systems BioMedicineResearch Institute, National Center for Child Health and DevelopmentTokyoJapan
| | - Kaoru Yoshida
- Department of Pediatric Hematology and Oncology ResearchResearch Institute, National Center for Child Health and DevelopmentTokyoJapan
| | - Ryota Shirai
- Department of Pediatric Hematology and Oncology ResearchResearch Institute, National Center for Child Health and DevelopmentTokyoJapan
- Department of Pediatrics, Graduate School of MedicineYokohama City UniversityYokohamaJapan
| | - Tomoo Osumi
- Department of Pediatric Hematology and Oncology ResearchResearch Institute, National Center for Child Health and DevelopmentTokyoJapan
- Children's Cancer CenterNational Center for Child Health and DevelopmentTokyoJapan
| | - Chikako Kiyotani
- Children's Cancer CenterNational Center for Child Health and DevelopmentTokyoJapan
| | - Yoko Shioda
- Children's Cancer CenterNational Center for Child Health and DevelopmentTokyoJapan
| | - Keita Terashima
- Children's Cancer CenterNational Center for Child Health and DevelopmentTokyoJapan
| | - Sae Ishimaru
- Department of Hematology/OncologyTokyo Metropolitan Children's Medical CenterTokyoJapan
- Trial and Data CenterPrincess Máxima Center for Pediatric OncologyUtrechtthe Netherlands
| | - Yuki Yuza
- Department of Hematology/OncologyTokyo Metropolitan Children's Medical CenterTokyoJapan
| | - Masatoshi Takagi
- Department of Pediatrics and Developmental BiologyGraduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU)TokyoJapan
| | - Yuki Arakawa
- Department of Hematology/OncologySaitama Children's Medical CenterSaitamaJapan
| | - Toshihiko Imamura
- Department of PediatricsKyoto Prefectural University of Medicine, Graduate School of Medical ScienceKyotoJapan
| | - Daisuke Hasegawa
- Department of PediatricsSt. Luke's International HospitalTokyoJapan
| | - Akiko Inoue
- Department of PediatricsOsaka Medical and Pharmaceutical UniversityTakatsukiJapan
| | - Takako Yoshioka
- Department of PathologyNational Center for Child Health and DevelopmentTokyoJapan
| | - Shuichi Ito
- Department of Pediatrics, Graduate School of MedicineYokohama City UniversityYokohamaJapan
| | - Daisuke Tomizawa
- Children's Cancer CenterNational Center for Child Health and DevelopmentTokyoJapan
| | - Katsuyoshi Koh
- Department of Hematology/OncologySaitama Children's Medical CenterSaitamaJapan
| | - Kimikazu Matsumoto
- Children's Cancer CenterNational Center for Child Health and DevelopmentTokyoJapan
| | - Nobutaka Kiyokawa
- Department of Pediatric Hematology and Oncology ResearchResearch Institute, National Center for Child Health and DevelopmentTokyoJapan
| | - Seishi Ogawa
- Department of Pathology and Tumor BiologyGraduate School of Medicine, Kyoto UniversityKyotoJapan
| | - Atsushi Manabe
- Department of PediatricsHokkaido University Graduate School of MedicineSapporoJapan
| | - Akira Niwa
- Department of Clinical Application, Center for iPS Cell Research and ApplicationKyoto UniversityKyotoJapan
| | - Kenichiro Hata
- Department of Maternal‐Fetal BiologyResearch Institute, National Center for Child Health and DevelopmentTokyoJapan
- Department of Human Molecular Genetics, Gunma University Graduate School of MedicineMaebashiJapan
| | - Jun J. Yang
- Department of Pharmacy and Pharmaceutical SciencesSt. Jude Children's Research HospitalTennesseeMemphisUSA
- Department of OncologySt. Jude Children's Research HospitalMemphisUSA
| | - Motohiro Kato
- Department of Pediatric Hematology and Oncology ResearchResearch Institute, National Center for Child Health and DevelopmentTokyoJapan
- Children's Cancer CenterNational Center for Child Health and DevelopmentTokyoJapan
- Department of PediatricsThe University of TokyoTokyoJapan
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37
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Teng JY, Yang DP, Tang C, Fang HS, Sun HY, Xiang YN, Li XM, Yang F, Xia RX, Fan F, Liu J, Yu J, Hu JC, Li BS, Li H, Meng FL, Duan CW, Zhou BBS. Targeting DNA polymerase β elicits synthetic lethality with mismatch repair deficiency in acute lymphoblastic leukemia. Leukemia 2023:10.1038/s41375-023-01902-3. [PMID: 37095208 DOI: 10.1038/s41375-023-01902-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 03/26/2023] [Accepted: 04/12/2023] [Indexed: 04/26/2023]
Abstract
Mismatch repair (MMR) deficiency has been linked to thiopurine resistance and hypermutation in relapsed acute lymphoblastic leukemia (ALL). However, the repair mechanism of thiopurine-induced DNA damage in the absence of MMR remains unclear. Here, we provide evidence that DNA polymerase β (POLB) of base excision repair (BER) pathway plays a critical role in the survival and thiopurine resistance of MMR-deficient ALL cells. In these aggressive resistant ALL cells, POLB depletion and its inhibitor oleanolic acid (OA) treatment result in synthetic lethality with MMR deficiency through increased cellular apurinic/apyrimidinic (AP) sites, DNA strand breaks and apoptosis. POLB depletion increases thiopurine sensitivities of resistant cells, and OA synergizes with thiopurine to kill these cells in ALL cell lines, patient-derived xenograft (PDX) cells and xenograft mouse models. Our findings suggest BER and POLB's roles in the process of repairing thiopurine-induced DNA damage in MMR-deficient ALL cells, and implicate their potentials as therapeutic targets against aggressive ALL progression.
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Affiliation(s)
- Ji-Yuan Teng
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ding-Peng Yang
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Chao Tang
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hou-Shun Fang
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hui-Ying Sun
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yue-Ning Xiang
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Xiao-Meng Li
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fan Yang
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Rui-Xue Xia
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fu Fan
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jingjing Liu
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jiyang Yu
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jin-Chuan Hu
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Ben-Shang Li
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hui Li
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fei-Long Meng
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Cai-Wen Duan
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Bin-Bing S Zhou
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Department of Pharmacology and Chemical Biology, School of Basic Medicine and Collaborative Innovation Center for Translational Medicine, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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38
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Donker HC, van Es B, Tamminga M, Lunter GA, van Kempen LCLT, Schuuring E, Hiltermann TJN, Groen HJM. Using genomic scars to select immunotherapy beneficiaries in advanced non-small cell lung cancer. Sci Rep 2023; 13:6581. [PMID: 37085581 PMCID: PMC10121673 DOI: 10.1038/s41598-023-32499-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 03/28/2023] [Indexed: 04/23/2023] Open
Abstract
In advanced non-small cell lung cancer (NSCLC), response to immunotherapy is difficult to predict from pre-treatment information. Given the toxicity of immunotherapy and its financial burden on the healthcare system, we set out to identify patients for whom treatment is effective. To this end, we used mutational signatures from DNA mutations in pre-treatment tissue. Single base substitutions, doublet base substitutions, indels, and copy number alteration signatures were analysed in [Formula: see text] patients (the discovery set). We found that tobacco smoking signature (SBS4) and thiopurine chemotherapy exposure-associated signature (SBS87) were linked to durable benefit. Combining both signatures in a machine learning model separated patients with a progression-free survival hazard ratio of 0.40[Formula: see text] on the cross-validated discovery set and 0.24[Formula: see text] on an independent external validation set ([Formula: see text]). This paper demonstrates that the fingerprints of mutagenesis, codified through mutational signatures, select advanced NSCLC patients who may benefit from immunotherapy, thus potentially reducing unnecessary patient burden.
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Affiliation(s)
- H C Donker
- Department of Pulmonary Diseases, University of Groningen, University Medical Centre Groningen, Hanzeplein 1, P.O. Box 30.001, 9700 RB, Groningen, The Netherlands
| | - B van Es
- Central Diagnostic Laboratory, University Medical Centre Utrecht, Utrecht University, Heidelberglaan 100, 3508 GA, Utrecht, The Netherlands.
- MedxAI, Theophile de Bockstraat 77-1, 1058 VA, Amsterdam, The Netherlands.
| | - M Tamminga
- Department of Pulmonary Diseases, University of Groningen, University Medical Centre Groningen, Hanzeplein 1, P.O. Box 30.001, 9700 RB, Groningen, The Netherlands
- Department of Internal Medicine, Twente Hospital, Enschede, The Netherlands
| | - G A Lunter
- Department of Epidemiology, University of Groningen, University Medical Centre Groningen, 9713 GZ, Groningen, The Netherlands
| | - L C L T van Kempen
- Department Of Pathology, University of Antwerp, University Hospital Antwerp, 2650, Edegem, Belgium
| | - E Schuuring
- Department of Pathology and Medical Biology, University of Groningen, University Medical Centre Groningen, Hanzeplein 1, P.O. Box 30.001, 9700 RB, Groningen, The Netherlands
| | - T J N Hiltermann
- Department of Pulmonary Diseases, University of Groningen, University Medical Centre Groningen, Hanzeplein 1, P.O. Box 30.001, 9700 RB, Groningen, The Netherlands
| | - H J M Groen
- Department of Pulmonary Diseases, University of Groningen, University Medical Centre Groningen, Hanzeplein 1, P.O. Box 30.001, 9700 RB, Groningen, The Netherlands
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39
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Liu Y, Klein J, Bajpai R, Dong L, Tran Q, Kolekar P, Smith JL, Ries RE, Huang BJ, Wang YC, Alonzo TA, Tian L, Mulder HL, Shaw TI, Ma J, Walsh MP, Song G, Westover T, Autry RJ, Gout AM, Wheeler DA, Wan S, Wu G, Yang JJ, Evans WE, Loh M, Easton J, Zhang J, Klco JM, Meshinchi S, Brown PA, Pruett-Miller SM, Ma X. Etiology of oncogenic fusions in 5,190 childhood cancers and its clinical and therapeutic implication. Nat Commun 2023; 14:1739. [PMID: 37019972 PMCID: PMC10076316 DOI: 10.1038/s41467-023-37438-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 03/16/2023] [Indexed: 04/07/2023] Open
Abstract
Oncogenic fusions formed through chromosomal rearrangements are hallmarks of childhood cancer that define cancer subtype, predict outcome, persist through treatment, and can be ideal therapeutic targets. However, mechanistic understanding of the etiology of oncogenic fusions remains elusive. Here we report a comprehensive detection of 272 oncogenic fusion gene pairs by using tumor transcriptome sequencing data from 5190 childhood cancer patients. We identify diverse factors, including translation frame, protein domain, splicing, and gene length, that shape the formation of oncogenic fusions. Our mathematical modeling reveals a strong link between differential selection pressure and clinical outcome in CBFB-MYH11. We discover 4 oncogenic fusions, including RUNX1-RUNX1T1, TCF3-PBX1, CBFA2T3-GLIS2, and KMT2A-AFDN, with promoter-hijacking-like features that may offer alternative strategies for therapeutic targeting. We uncover extensive alternative splicing in oncogenic fusions including KMT2A-MLLT3, KMT2A-MLLT10, C11orf95-RELA, NUP98-NSD1, KMT2A-AFDN and ETV6-RUNX1. We discover neo splice sites in 18 oncogenic fusion gene pairs and demonstrate that such splice sites confer therapeutic vulnerability for etiology-based genome editing. Our study reveals general principles on the etiology of oncogenic fusions in childhood cancer and suggests profound clinical implications including etiology-based risk stratification and genome-editing-based therapeutics.
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Affiliation(s)
- Yanling Liu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jonathon Klein
- Department of Cell and Molecular Biology and Center for Advanced Genome Editing, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Richa Bajpai
- Department of Cell and Molecular Biology and Center for Advanced Genome Editing, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Li Dong
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Quang Tran
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Pandurang Kolekar
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jenny L Smith
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Rhonda E Ries
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Benjamin J Huang
- Department of Pediatrics and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | | | - Todd A Alonzo
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Liqing Tian
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Heather L Mulder
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Timothy I Shaw
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | - Jing Ma
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael P Walsh
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Guangchun Song
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Tamara Westover
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Robert J Autry
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Alexander M Gout
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - David A Wheeler
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shibiao Wan
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Gang Wu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jun J Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - William E Evans
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mignon Loh
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute and the Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA, USA
| | - John Easton
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jeffery M Klco
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
| | | | - Shondra M Pruett-Miller
- Department of Cell and Molecular Biology and Center for Advanced Genome Editing, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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40
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Erikstein BS, Ahmed AB, Forthun RB, Leh F, Gjertsen BT, Reikvam H. Treatment and Response Evaluation Challenges in a Pregnant Woman With B-Cell Lymphoblastic Leukemia and Li-Fraumeni Syndrome. J Hematol 2023; 12:92-99. [PMID: 37187497 PMCID: PMC10181328 DOI: 10.14740/jh1107] [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: 02/25/2023] [Accepted: 04/19/2023] [Indexed: 05/17/2023] Open
Abstract
Li-Fraumeni syndrome (LFS) is a cancer predisposing syndrome caused by pathogenic germline TP53 gene mutations with important therapeutic and prognostic implications for many types of cancer. A small proportion of LFS patients develop B-cell lymphoblastic leukemia (B-ALL) in adult years. Standard treatment often proves inadequate, but immunotherapy has provided new treatment options. The current case report presents a pregnant woman with LFS and newly diagnosed B-ALL with hypodiploidy developed after treatment for early-onset breast cancer. We describe the treatment course, treatment-related complications and provide laboratory data crucial for evaluating and modifying treatment for this difficult clinical case. Our findings support the need for close collaboration between clinicians and experts on immunophenotyping. Through our report, we show that immunotherapy is feasible in patients with LFS and B-ALL, despite a poor initial response to induction therapy.
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Affiliation(s)
- Bjarte Skoe Erikstein
- Department of Immunology and Transfusion Medicine, Haukeland University Hospital, Bergen, Norway
- Corresponding Author: Bjarte Skoe Erikstein, Department of Immunology and Transfusion Medicine, Haukeland University Hospital, N-5021 Bergen, Norway.
| | - Aymen Bushra Ahmed
- Department of Medicine, Hematology Section, Haukeland University Hospital, Bergen, Norway
| | | | - Friedemann Leh
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Bjørn Tore Gjertsen
- Department of Medicine, Hematology Section, Haukeland University Hospital, Bergen, Norway
- Centre for Cancer Biomarkers, Department of Clinical Science, Precision Oncology Research Group, University of Bergen, Bergen, Norway
| | - Håkon Reikvam
- Department of Medicine, Hematology Section, Haukeland University Hospital, Bergen, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
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41
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Nguyen TTT, Tanaka Y, Sanada M, Hosaka M, Tamai M, Kagami K, Komatsu C, Somazu S, Harama D, Kasai S, Watanabe A, Akahane K, Goi K, Inukai T. CRISPR/Cas9-Mediated Induction of Relapse-Specific NT5C2 and PRPS1 Mutations Confers Thiopurine Resistance as a Relapsed Lymphoid Leukemia Model. Mol Pharmacol 2023; 103:199-210. [PMID: 36669880 DOI: 10.1124/molpharm.122.000546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 12/13/2022] [Accepted: 01/04/2023] [Indexed: 01/21/2023] Open
Abstract
6-Mercaptopurine (6-MP) is a key component in maintenance therapy for childhood acute lymphoblastic leukemia (ALL). Recent next-generation sequencing analysis of childhood ALL clarified the emergence of the relapse-specific mutations of the NT5C2 and PRPS1 genes, which are involved in thiopurine metabolism. In this scenario, minor clones of leukemia cells could acquire the 6-MP-resistant phenotype as a result of the NT5C2 or PRPS1 mutation during chemotherapy (including 6-MP treatment) and confer disease relapse after selective expansion. Thus, to establish new therapeutic modalities overcoming 6-MP resistance in relapsed ALL, human leukemia models with NT5C2 and PRPS1 mutations in the intrinsic genes are urgently required. Here, mimicking the initiation process of the above clinical course, we sought to induce two relapse-specific hotspot mutations (R39Q mutation of the NT5C2 gene and S103N mutation of the PRPS1 gene) into a human lymphoid leukemia cell line by homologous recombination (HR) using the CRISPR/Cas9 system. After 6-MP selection of the cells transfected with Cas9 combined with single-guide RNA and donor DNA templates specific for either of those two mutations, we obtained the sublines with the intended NT5C2-R39Q and PRPS1-S103N mutation as a result of HR. Moreover, diverse in-frame small insertion/deletions were also confirmed in the 6-MP-resistant sublines at the target sites of the NT5C2 and PRPS1 genes as a result of nonhomologous end joining. These sublines are useful for molecular pharmacological evaluation of the NT5C2 and PRPS1 gene mutations in the 6-MP sensitivity and development of therapy overcoming the thiopurine resistance of leukemia cells. SIGNIFICANCE STATEMENT: Mimicking the initiation process of relapse-specific mutations of the NT5C2 and PRPS1 genes in childhood acute lymphoblastic leukemia treated with 6-mercaptopurine (6-MP), this study sought to introduce NT5C2-R39Q and PRPS1-S103N mutations into a human lymphoid leukemia cell line by homologous recombination using the CRISPR/Cas9 system. In the resultant 6-MP-resistant sublines, the intended mutations and diverse in-frame small insertions/deletions were confirmed, indicating that the obtained sublines are useful for molecular pharmacological evaluation of the NT5C2 and PRPS1 gene mutations.
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Affiliation(s)
- Thao Thu Thi Nguyen
- Department of Pediatrics, University of Yamanashi, Yamanashi, Japan (T.T.T.N., M.T., K.K., C.K., S.S., D.H., S.K., A.W., K.A., K.G., T.I.); Division of Medicinal Safety Science, National Institutes of Health Sciences, Kanagawa, Japan (Y.T.); and Advanced Diagnostic Research Department, Clinical Research Center, National Hospital Organization, Nagoya Medical Center, Japan (M.S., M.H.)
| | - Yoichi Tanaka
- Department of Pediatrics, University of Yamanashi, Yamanashi, Japan (T.T.T.N., M.T., K.K., C.K., S.S., D.H., S.K., A.W., K.A., K.G., T.I.); Division of Medicinal Safety Science, National Institutes of Health Sciences, Kanagawa, Japan (Y.T.); and Advanced Diagnostic Research Department, Clinical Research Center, National Hospital Organization, Nagoya Medical Center, Japan (M.S., M.H.)
| | - Masashi Sanada
- Department of Pediatrics, University of Yamanashi, Yamanashi, Japan (T.T.T.N., M.T., K.K., C.K., S.S., D.H., S.K., A.W., K.A., K.G., T.I.); Division of Medicinal Safety Science, National Institutes of Health Sciences, Kanagawa, Japan (Y.T.); and Advanced Diagnostic Research Department, Clinical Research Center, National Hospital Organization, Nagoya Medical Center, Japan (M.S., M.H.)
| | - Masumi Hosaka
- Department of Pediatrics, University of Yamanashi, Yamanashi, Japan (T.T.T.N., M.T., K.K., C.K., S.S., D.H., S.K., A.W., K.A., K.G., T.I.); Division of Medicinal Safety Science, National Institutes of Health Sciences, Kanagawa, Japan (Y.T.); and Advanced Diagnostic Research Department, Clinical Research Center, National Hospital Organization, Nagoya Medical Center, Japan (M.S., M.H.)
| | - Minori Tamai
- Department of Pediatrics, University of Yamanashi, Yamanashi, Japan (T.T.T.N., M.T., K.K., C.K., S.S., D.H., S.K., A.W., K.A., K.G., T.I.); Division of Medicinal Safety Science, National Institutes of Health Sciences, Kanagawa, Japan (Y.T.); and Advanced Diagnostic Research Department, Clinical Research Center, National Hospital Organization, Nagoya Medical Center, Japan (M.S., M.H.)
| | - Keiko Kagami
- Department of Pediatrics, University of Yamanashi, Yamanashi, Japan (T.T.T.N., M.T., K.K., C.K., S.S., D.H., S.K., A.W., K.A., K.G., T.I.); Division of Medicinal Safety Science, National Institutes of Health Sciences, Kanagawa, Japan (Y.T.); and Advanced Diagnostic Research Department, Clinical Research Center, National Hospital Organization, Nagoya Medical Center, Japan (M.S., M.H.)
| | - Chiaki Komatsu
- Department of Pediatrics, University of Yamanashi, Yamanashi, Japan (T.T.T.N., M.T., K.K., C.K., S.S., D.H., S.K., A.W., K.A., K.G., T.I.); Division of Medicinal Safety Science, National Institutes of Health Sciences, Kanagawa, Japan (Y.T.); and Advanced Diagnostic Research Department, Clinical Research Center, National Hospital Organization, Nagoya Medical Center, Japan (M.S., M.H.)
| | - Shinpei Somazu
- Department of Pediatrics, University of Yamanashi, Yamanashi, Japan (T.T.T.N., M.T., K.K., C.K., S.S., D.H., S.K., A.W., K.A., K.G., T.I.); Division of Medicinal Safety Science, National Institutes of Health Sciences, Kanagawa, Japan (Y.T.); and Advanced Diagnostic Research Department, Clinical Research Center, National Hospital Organization, Nagoya Medical Center, Japan (M.S., M.H.)
| | - Daisuke Harama
- Department of Pediatrics, University of Yamanashi, Yamanashi, Japan (T.T.T.N., M.T., K.K., C.K., S.S., D.H., S.K., A.W., K.A., K.G., T.I.); Division of Medicinal Safety Science, National Institutes of Health Sciences, Kanagawa, Japan (Y.T.); and Advanced Diagnostic Research Department, Clinical Research Center, National Hospital Organization, Nagoya Medical Center, Japan (M.S., M.H.)
| | - Shin Kasai
- Department of Pediatrics, University of Yamanashi, Yamanashi, Japan (T.T.T.N., M.T., K.K., C.K., S.S., D.H., S.K., A.W., K.A., K.G., T.I.); Division of Medicinal Safety Science, National Institutes of Health Sciences, Kanagawa, Japan (Y.T.); and Advanced Diagnostic Research Department, Clinical Research Center, National Hospital Organization, Nagoya Medical Center, Japan (M.S., M.H.)
| | - Atsushi Watanabe
- Department of Pediatrics, University of Yamanashi, Yamanashi, Japan (T.T.T.N., M.T., K.K., C.K., S.S., D.H., S.K., A.W., K.A., K.G., T.I.); Division of Medicinal Safety Science, National Institutes of Health Sciences, Kanagawa, Japan (Y.T.); and Advanced Diagnostic Research Department, Clinical Research Center, National Hospital Organization, Nagoya Medical Center, Japan (M.S., M.H.)
| | - Koushi Akahane
- Department of Pediatrics, University of Yamanashi, Yamanashi, Japan (T.T.T.N., M.T., K.K., C.K., S.S., D.H., S.K., A.W., K.A., K.G., T.I.); Division of Medicinal Safety Science, National Institutes of Health Sciences, Kanagawa, Japan (Y.T.); and Advanced Diagnostic Research Department, Clinical Research Center, National Hospital Organization, Nagoya Medical Center, Japan (M.S., M.H.)
| | - Kumiko Goi
- Department of Pediatrics, University of Yamanashi, Yamanashi, Japan (T.T.T.N., M.T., K.K., C.K., S.S., D.H., S.K., A.W., K.A., K.G., T.I.); Division of Medicinal Safety Science, National Institutes of Health Sciences, Kanagawa, Japan (Y.T.); and Advanced Diagnostic Research Department, Clinical Research Center, National Hospital Organization, Nagoya Medical Center, Japan (M.S., M.H.)
| | - Takeshi Inukai
- Department of Pediatrics, University of Yamanashi, Yamanashi, Japan (T.T.T.N., M.T., K.K., C.K., S.S., D.H., S.K., A.W., K.A., K.G., T.I.); Division of Medicinal Safety Science, National Institutes of Health Sciences, Kanagawa, Japan (Y.T.); and Advanced Diagnostic Research Department, Clinical Research Center, National Hospital Organization, Nagoya Medical Center, Japan (M.S., M.H.)
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42
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Woodward EL, Yang M, Moura-Castro LH, van den Bos H, Gunnarsson R, Olsson-Arvidsson L, Spierings DCJ, Castor A, Duployez N, Zaliova M, Zuna J, Johansson B, Foijer F, Paulsson K. Clonal origin and development of high hyperdiploidy in childhood acute lymphoblastic leukaemia. Nat Commun 2023; 14:1658. [PMID: 36966135 PMCID: PMC10039905 DOI: 10.1038/s41467-023-37356-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 03/14/2023] [Indexed: 03/27/2023] Open
Abstract
High hyperdiploid acute lymphoblastic leukemia (HeH ALL), one of the most common childhood malignancies, is driven by nonrandom aneuploidy (abnormal chromosome numbers) mainly comprising chromosomal gains. In this study, we investigate how aneuploidy in HeH ALL arises. Single cell whole genome sequencing of 2847 cells from nine primary cases and one normal bone marrow reveals that HeH ALL generally display low chromosomal heterogeneity, indicating that they are not characterized by chromosomal instability and showing that aneuploidy-driven malignancies are not necessarily chromosomally heterogeneous. Furthermore, most chromosomal gains are present in all leukemic cells, suggesting that they arose early during leukemogenesis. Copy number data from 577 primary cases reveals selective pressures that were used for in silico modeling of aneuploidy development. This shows that the aneuploidy in HeH ALL likely arises by an initial tripolar mitosis in a diploid cell followed by clonal evolution, in line with a punctuated evolution model.
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Affiliation(s)
- Eleanor L Woodward
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Minjun Yang
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Larissa H Moura-Castro
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Hilda van den Bos
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Rebeqa Gunnarsson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Linda Olsson-Arvidsson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
- Department of Clinical Genetics, Pathology, and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
| | - Diana C J Spierings
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Anders Castor
- Department of Pediatrics, Skåne University Hospital, Lund University, Lund, Sweden
| | - Nicolas Duployez
- Laboratory of Hematology, Centre Hospitalier Universitaire (CHU) Lille, Lille, France
- Unité Mixte de Recherche en Santé (UMR-S) 1172, INSERM/University of Lille, Lille, France
| | - Marketa Zaliova
- Department of Pediatric Hematology and Oncology, Second Faculty of Medicine, Charles University/University Hospital Motol, Prague, Czech Republic
- Childhood Leukaemia Investigation Prague (CLIP), Prague, Czech Republic
| | - Jan Zuna
- Department of Pediatric Hematology and Oncology, Second Faculty of Medicine, Charles University/University Hospital Motol, Prague, Czech Republic
- Childhood Leukaemia Investigation Prague (CLIP), Prague, Czech Republic
| | - Bertil Johansson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
- Department of Clinical Genetics, Pathology, and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
| | - Floris Foijer
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Kajsa Paulsson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden.
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43
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Patterson A, Elbasir A, Tian B, Auslander N. Computational Methods Summarizing Mutational Patterns in Cancer: Promise and Limitations for Clinical Applications. Cancers (Basel) 2023; 15:cancers15071958. [PMID: 37046619 PMCID: PMC10093138 DOI: 10.3390/cancers15071958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 02/24/2023] [Accepted: 03/09/2023] [Indexed: 03/29/2023] Open
Abstract
Since the rise of next-generation sequencing technologies, the catalogue of mutations in cancer has been continuously expanding. To address the complexity of the cancer-genomic landscape and extract meaningful insights, numerous computational approaches have been developed over the last two decades. In this review, we survey the current leading computational methods to derive intricate mutational patterns in the context of clinical relevance. We begin with mutation signatures, explaining first how mutation signatures were developed and then examining the utility of studies using mutation signatures to correlate environmental effects on the cancer genome. Next, we examine current clinical research that employs mutation signatures and discuss the potential use cases and challenges of mutation signatures in clinical decision-making. We then examine computational studies developing tools to investigate complex patterns of mutations beyond the context of mutational signatures. We survey methods to identify cancer-driver genes, from single-driver studies to pathway and network analyses. In addition, we review methods inferring complex combinations of mutations for clinical tasks and using mutations integrated with multi-omics data to better predict cancer phenotypes. We examine the use of these tools for either discovery or prediction, including prediction of tumor origin, treatment outcomes, prognosis, and cancer typing. We further discuss the main limitations preventing widespread clinical integration of computational tools for the diagnosis and treatment of cancer. We end by proposing solutions to address these challenges using recent advances in machine learning.
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Affiliation(s)
- Andrew Patterson
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- The Wistar Institute, Philadelphia, PA 19104, USA
| | | | - Bin Tian
- The Wistar Institute, Philadelphia, PA 19104, USA
| | - Noam Auslander
- The Wistar Institute, Philadelphia, PA 19104, USA
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Correspondence:
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44
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Ji X, Wang E, Cui Q. Deciphering gene contributions and etiologies of somatic mutational signatures of cancer. Brief Bioinform 2023; 24:6995381. [PMID: 36682004 DOI: 10.1093/bib/bbad017] [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: 07/27/2022] [Revised: 12/15/2022] [Accepted: 01/04/2023] [Indexed: 01/23/2023] Open
Abstract
Somatic mutational signatures (MSs) identified by genome sequencing play important roles in exploring the cause and development of cancer. Thus far, many such signatures have been identified, and some of them do imply causes of cancer. However, a major bottleneck is that we do not know the potential meanings (i.e. carcinogenesis or biological functions) and contributing genes for most of them. Here, we presented a computational framework, Gene Somatic Genome Pattern (GSGP), which can decipher the molecular mechanisms of the MSs. More importantly, it is the first time that the GSGP is able to process MSs from ribonucleic acid (RNA) sequencing, which greatly extended the applications of both MS analysis and RNA sequencing (RNAseq). As a result, GSGP analyses match consistently with previous reports and identify the etiologies for a number of novel signatures. Notably, we applied GSGP to RNAseq data and revealed an RNA-derived MS involved in deficient deoxyribonucleic acid mismatch repair and microsatellite instability in colorectal cancer. Researchers can perform customized GSGP analysis using the web tools or scripts we provide.
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Affiliation(s)
- Xiangwen Ji
- Department of Biomedical Informatics, School of Basic Medical Science, Peking University Health Science Center, Beijing, China
| | - Edwin Wang
- Department of Biochemistry and Molecular Biology, Medical Genetics, and Oncology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Qinghua Cui
- Department of Biomedical Informatics, School of Basic Medical Science, Peking University Health Science Center, Beijing, China
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Chen TM, Huang CM, Setiawan SA, Hsieh MS, Sheen CC, Yeh CT. KDM5D Histone Demethylase Identifies Platinum-Tolerant Head and Neck Cancer Cells Vulnerable to Mitotic Catastrophe. Int J Mol Sci 2023; 24:ijms24065310. [PMID: 36982384 PMCID: PMC10049674 DOI: 10.3390/ijms24065310] [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: 01/15/2023] [Revised: 02/27/2023] [Accepted: 03/06/2023] [Indexed: 03/12/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is a major contributor to cancer incidence globally and is currently managed by surgical resection followed by adjuvant chemoradiotherapy. However, local recurrence is the major cause of mortality, indicating the emergence of drug-tolerant persister cells. A specific histone demethylase, namely lysine-specific demethylase 5D (KDM5D), is overexpressed in diverse types of cancers and involved in cancer cell cycle regulation. However, the role of KDM5D in the development of cisplatin-tolerant persister cells remains unexplored. Here, we demonstrated that KDM5D contributes to the development of persister cells. Aurora Kinase B (AURKB) disruption affected the vulnerability of persister cells in a mitotic catastrophe–dependent manner. Comprehensive in silico, in vitro, and in vivo experiments were performed. KDM5D expression was upregulated in HNSCC tumor cells, cancer stem cells, and cisplatin-resistant cells with biologically distinct signaling alterations. In an HNSCC cohort, high KDM5D expression was associated with a poor response to platinum treatment and early disease recurrence. KDM5D knockdown reduced the tolerance of persister cells to platinum agents and caused marked cell cycle deregulation, including the loss of DNA damage prevention, and abnormal mitosis-enhanced cell cycle arrest. By modulating mRNA levels of AURKB, KDM5D promoted the generation of platinum-tolerant persister cells in vitro, leading to the identification of the KDM5D/AURKB axis, which regulates cancer stemness and drug tolerance of HNSCC. Treatment with an AURKB inhibitor, namely barasertib, resulted in a lethal consequence of mitotic catastrophe in HNSCC persister cells. The cotreatment of cisplatin and barasertib suppressed tumor growth in the tumor mouse model. Thus, KDM5D might be involved in the development of persister cells, and AURKB disruption can overcome tolerance to platinum treatment in HNSCC.
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Affiliation(s)
- Tsung-Ming Chen
- Department of Otolaryngology, School of Medicine, College of Medicine, Taipei Medical University, Taipei City 11031, Taiwan;
- Department of Otolaryngology-Head and Neck Surgery, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
| | - Chih-Ming Huang
- Department of Otolaryngology, Taitung Mackay Memorial Hospital, Taitung City 950408, Taiwan;
- Department of Nursing, Tajen University, Pingtung 90741, Taiwan
| | - Syahru Agung Setiawan
- International Ph.D. Program in Medicine, College of Medicine, Taipei Medical University, Taipei City 11031, Taiwan;
- Department of Medical Research & Education, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
| | - Ming-Shou Hsieh
- School of Dentistry, College of Oral Medicine, Taipei Medical University, Taipei City 110, Taiwan;
- Department of Dentistry, Shuang Ho Hospital, Taipei Medical University, New Taipei City, 235, Taiwan
- Department of Periodontics, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
| | - Chih-Chi Sheen
- School of Dentistry, College of Oral Medicine, Taipei Medical University, Taipei City 110, Taiwan;
- Department of Dentistry, Shuang Ho Hospital, Taipei Medical University, New Taipei City, 235, Taiwan
- Department of Periodontics, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
- Correspondence: (C.-C.S.); (C.-T.Y.); Tel.: +886-2-249-0088 (ext. 8885) (C.-C.S.); +886-2-249-0088 (ext. 8881) (C.-T.Y.); Fax: +886-2-2248-0900 (C.-C.S.); +886-2-2248-0900 (C.-T.Y.)
| | - Chi-Tai Yeh
- Department of Medical Research & Education, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
- Continuing Education Program of Food Biotechnology Applications, College of Science and Engineering, National Taitung University, Taitung 95092, Taiwan
- Correspondence: (C.-C.S.); (C.-T.Y.); Tel.: +886-2-249-0088 (ext. 8885) (C.-C.S.); +886-2-249-0088 (ext. 8881) (C.-T.Y.); Fax: +886-2-2248-0900 (C.-C.S.); +886-2-2248-0900 (C.-T.Y.)
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46
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Jahn J, Diamond B, Hsu J, Montoya S, Totiger TM, Landgren O, Maura F, Taylor J. Therapy-selected clonal hematopoiesis and its role in myeloid neoplasms. Leuk Res 2023; 126:107020. [PMID: 36696829 PMCID: PMC11305114 DOI: 10.1016/j.leukres.2023.107020] [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: 11/22/2022] [Revised: 01/06/2023] [Accepted: 01/19/2023] [Indexed: 01/21/2023]
Abstract
Therapy-related myeloid neoplasms (t-MN) account for approximately 10-15% of all myeloid neoplasms and are associated with poor prognosis. Genomic characterization of t-MN to date has been limited in comparison to the considerable sequencing efforts performed for de novo myeloid neoplasms. Until recently, targeted deep sequencing (TDS) or whole exome sequencing (WES) have been the primary technologies utilized and thus limited the ability to explore the landscape of structural variants and mutational signatures. In the past decade, population-level studies have identified clonal hematopoiesis as a risk factor for the development of myeloid neoplasms. However, emerging research on clonal hematopoiesis as a risk factor for developing t-MN is evolving, and much is unknown about the progression of CH to t-MN. In this work, we will review the current knowledge of the genomic landscape of t-MN, discuss background knowledge of clonal hematopoiesis gained from studies of de novo myeloid neoplasms, and examine the recent literature studying the role of therapeutic selection of CH and its evolution under the effects of antineoplastic therapy. Finally, we will discuss the potential implications on current clinical practice and the areas of focus needed for future research into therapy-selected clonal hematopoiesis in myeloid neoplasms.
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Affiliation(s)
- Jacob Jahn
- Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, United States
| | - Benjamin Diamond
- Myeloma Division, Department of Medicine, University of Miami Miller School of Medicine, United States
| | - Jeffrey Hsu
- Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, United States
| | - Skye Montoya
- Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, United States
| | - Tulasigeri M Totiger
- Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, United States
| | - Ola Landgren
- Myeloma Division, Department of Medicine, University of Miami Miller School of Medicine, United States
| | - Francesco Maura
- Myeloma Division, Department of Medicine, University of Miami Miller School of Medicine, United States
| | - Justin Taylor
- Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, United States; Leukemia Program, Department of Medicine, University of Miami Miller School of Medicine, United States.
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47
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Thakur R, Bhatia P, Singh M, Sreedharanunni S, Sharma P, Singh A, Trehan A. Therapy-Acquired Clonal Mutations in Thiopurine Drug-Response Genes Drive Majority of Early Relapses in Pediatric B-Cell Precursor Acute Lymphoblastic Leukemia. Diagnostics (Basel) 2023; 13:diagnostics13050884. [PMID: 36900028 PMCID: PMC10001400 DOI: 10.3390/diagnostics13050884] [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: 01/19/2023] [Revised: 02/15/2023] [Accepted: 02/24/2023] [Indexed: 03/02/2023] Open
Abstract
METHODS Forty pediatric (0-12 years) B-ALL DNA samples (20 paired Diagnosis-Relapse) and an additional six B-ALL DNA samples (without relapse at 3 years post treatment), as the non-relapse arm, were retrieved from the biobank for advanced genomic analysis. Deep sequencing (1050-5000X; mean 1600X) was performed using a custom NGS panel of 74 genes incorporating unique molecular barcodes. RESULTS A total 47 major clones (>25% VAF) and 188 minor clones were noted in 40 cases after bioinformatic data filtering. Of the forty-seven major clones, eight (17%) were diagnosis-specific, seventeen (36%) were relapse-specific and 11 (23%) were shared. In the control arm, no pathogenic major clone was noted in any of the six samples. The most common clonal evolution pattern observed was therapy-acquired (TA), with 9/20 (45%), followed by M-M, with 5/20 (25%), m-M, with 4/20 (20%) and unclassified (UNC) 2/20 (10%). The TA clonal pattern was predominant in early relapses 7/12 (58%), with 71% (5/7) having major clonal mutations in the NT5C2 or PMS2 gene related to thiopurine-dose response. In addition, 60% (3/5) of these cases were preceded by an initial hit in the epigenetic regulator, KMT2D. Mutations in common relapse-enriched genes comprised 33% of the very early relapses, 50% of the early and 40% of the late relapses. Overall, 14/46 (30%) of the samples showed the hypermutation phenotype, of which the majority (50%) had a TA pattern of relapse. CONCLUSIONS Our study highlights the high frequency of early relapses driven by TA clones, demonstrating the need to identify their early rise during chemotherapy by digital PCR.
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Affiliation(s)
- Rozy Thakur
- Pediatric Hematology Oncology Unit, Department of Pediatrics, Advanced Pediatric Centre, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Prateek Bhatia
- Pediatric Hematology Oncology Unit, Department of Pediatrics, Advanced Pediatric Centre, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
- Correspondence: ; Tel.: +91-0172-2755329
| | - Minu Singh
- Pediatric Hematology Oncology Unit, Department of Pediatrics, Advanced Pediatric Centre, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Sreejesh Sreedharanunni
- Department of Haematology, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Pankaj Sharma
- Pediatric Hematology Oncology Unit, Department of Pediatrics, Advanced Pediatric Centre, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Aditya Singh
- Department of Cardiovascular Medicine, Stanford University, Stanford, CA 94305, USA
| | - Amita Trehan
- Pediatric Hematology Oncology Unit, Department of Pediatrics, Advanced Pediatric Centre, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
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48
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Thatikonda V, Islam SMA, Autry RJ, Jones BC, Gröbner SN, Warsow G, Hutter B, Huebschmann D, Fröhling S, Kool M, Blattner-Johnson M, Jones DTW, Alexandrov LB, Pfister SM, Jäger N. Comprehensive analysis of mutational signatures reveals distinct patterns and molecular processes across 27 pediatric cancers. NATURE CANCER 2023; 4:276-289. [PMID: 36702933 PMCID: PMC9970869 DOI: 10.1038/s43018-022-00509-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 12/21/2022] [Indexed: 01/27/2023]
Abstract
Analysis of mutational signatures can reveal underlying molecular mechanisms of the processes that have imprinted the somatic mutations found in cancer genomes. Here, we analyze single base substitutions and small insertions and deletions in pediatric cancers encompassing 785 whole-genome sequenced tumors from 27 molecularly defined cancer subtypes. We identified only a small number of mutational signatures active in pediatric cancers, compared with previously analyzed adult cancers. Further, we report a significant difference in the proportion of pediatric tumors showing homologous recombination repair defect signatures compared with previous analyses. In pediatric leukemias, we identified an indel signature, not previously reported, characterized by long insertions in nonrepeat regions, affecting mainly intronic and intergenic regions, but also exons of known cancer genes. We provide a systematic overview of COSMIC v.3 mutational signatures active across pediatric cancers, which is highly relevant for understanding tumor biology and enabling future research in defining biomarkers of treatment response.
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Affiliation(s)
- Venu Thatikonda
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Global Computational Biology and Digital Sciences, Boehringer Ingelheim RCV GmbH, Vienna, Austria
| | - S M Ashiqul Islam
- Department of Cellular and Molecular Medicine and Department of Bioengineering, Moores Cancer Center, UC San Diego, La Jolla, CA, USA
| | - Robert J Autry
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Barbara C Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
- Pediatric Glioma Research Group, DKFZ, Heidelberg, Germany
| | - Susanne N Gröbner
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Gregor Warsow
- Omics IT and Data Management Core Facility (W610), DKFZ, Heidelberg, Germany
| | - Barbara Hutter
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Computational Oncology Group, Molecular Precision Oncology Program, National Center for Tumor Diseases (NCT) Heidelberg, DKFZ, Heidelberg, Germany
- Division of Applied Bioinformatics, DKFZ, Heidelberg, Germany
| | - Daniel Huebschmann
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Computational Oncology Group, Molecular Precision Oncology Program, National Center for Tumor Diseases (NCT) Heidelberg, DKFZ, Heidelberg, Germany
- Pattern Recognition and Digital Medicine, Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany
| | - Stefan Fröhling
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Division of Translational Medical Oncology, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Mirjam Blattner-Johnson
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Pediatric Glioma Research Group, DKFZ, Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Pediatric Glioma Research Group, DKFZ, Heidelberg, Germany
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine and Department of Bioengineering, Moores Cancer Center, UC San Diego, La Jolla, CA, USA
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- German Cancer Consortium (DKTK), Heidelberg, Germany.
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany.
| | - Natalie Jäger
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- German Cancer Consortium (DKTK), Heidelberg, Germany.
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Eadie LN, Rehn JA, Breen J, Osborn MP, Jessop S, Downes CEJ, Heatley SL, McClure BJ, Yeung DT, Revesz T, Saxon B, White DL. Case Report: Rare IKZF1 Gene Fusions Identified in Neonate with Congenital KMT2A-Rearranged Acute Lymphoblastic Leukemia. Genes (Basel) 2023; 14:genes14020264. [PMID: 36833191 PMCID: PMC9956107 DOI: 10.3390/genes14020264] [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: 12/13/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023] Open
Abstract
Chromosomal rearrangements involving the KMT2A gene occur frequently in acute lymphoblastic leukaemia (ALL). KMT2A-rearranged ALL (KMT2Ar ALL) has poor long-term survival rates and is the most common ALL subtype in infants less than 1 year of age. KMT2Ar ALL frequently occurs with additional chromosomal abnormalities including disruption of the IKZF1 gene, usually by exon deletion. Typically, KMT2Ar ALL in infants is accompanied by a limited number of cooperative le-sions. Here we report a case of aggressive infant KMT2Ar ALL harbouring additional rare IKZF1 gene fusions. Comprehensive genomic and transcriptomic analyses were performed on sequential samples. This report highlights the genomic complexity of this particular disease and describes the novel gene fusions IKZF1::TUT1 and KDM2A::IKZF1.
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Affiliation(s)
- Laura N. Eadie
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute, Adelaide, SA 5000, Australia
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia
| | - Jacqueline A. Rehn
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute, Adelaide, SA 5000, Australia
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia
| | - James Breen
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia
- South Australian Genomics Centre (SAGC), Adelaide, SA 5000, Australia
- Robinson Research Institute, University of Adelaide, Adelaide, SA 5006, Australia
| | - Michael P. Osborn
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia
- Australian & New Zealand Children’s Haematology/Oncology Group, Clayton, VIC 3168, Australia
- Australasian Leukaemia & Lymphoma Group, Richmond, VIC 3121, Australia
- Department of Haematology & Oncology, Women’s & Children’s Hospital, Adelaide, SA 5000, Australia
- Royal Adelaide Hospital, Adelaide, SA 5000, Australia
| | - Sophie Jessop
- Australian & New Zealand Children’s Haematology/Oncology Group, Clayton, VIC 3168, Australia
- Department of Haematology & Oncology, Women’s & Children’s Hospital, Adelaide, SA 5000, Australia
| | - Charlotte E. J. Downes
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute, Adelaide, SA 5000, Australia
- Faculty of Sciences, Engineering and Technology, University of Adelaide, Adelaide, SA 5000, Australia
| | - Susan L. Heatley
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute, Adelaide, SA 5000, Australia
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia
- Australian & New Zealand Children’s Haematology/Oncology Group, Clayton, VIC 3168, Australia
| | - Barbara J. McClure
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute, Adelaide, SA 5000, Australia
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia
| | - David T. Yeung
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute, Adelaide, SA 5000, Australia
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia
- Australasian Leukaemia & Lymphoma Group, Richmond, VIC 3121, Australia
- Royal Adelaide Hospital, Adelaide, SA 5000, Australia
| | - Tamas Revesz
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia
- Australian & New Zealand Children’s Haematology/Oncology Group, Clayton, VIC 3168, Australia
- Department of Haematology & Oncology, Women’s & Children’s Hospital, Adelaide, SA 5000, Australia
| | - Benjamin Saxon
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia
- Department of Haematology & Oncology, Women’s & Children’s Hospital, Adelaide, SA 5000, Australia
- Clinical Services and Research Division, Australian Red Cross Blood Service, Adelaide, SA 5000, Australia
| | - Deborah L. White
- Blood Cancer Program, Precision Cancer Medicine Theme, South Australian Health & Medical Research Institute, Adelaide, SA 5000, Australia
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia
- Australian & New Zealand Children’s Haematology/Oncology Group, Clayton, VIC 3168, Australia
- Australasian Leukaemia & Lymphoma Group, Richmond, VIC 3121, Australia
- Faculty of Sciences, Engineering and Technology, University of Adelaide, Adelaide, SA 5000, Australia
- Australian Genomics Health Alliance, Parkville, VIC 3052, Australia
- Correspondence:
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50
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Pancotti C, Rollo C, Birolo G, Benevenuta S, Fariselli P, Sanavia T. Unravelling the instability of mutational signatures extraction via archetypal analysis. Front Genet 2023; 13:1049501. [PMID: 36685831 PMCID: PMC9846778 DOI: 10.3389/fgene.2022.1049501] [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: 09/20/2022] [Accepted: 12/07/2022] [Indexed: 01/06/2023] Open
Abstract
The high cosine similarity between some single-base substitution mutational signatures and their characteristic flat profiles could suggest the presence of overfitting and mathematical artefacts. The newest version (v3.3) of the signature database available in the Catalogue Of Somatic Mutations In Cancer (COSMIC) provides a collection of 79 mutational signatures, which has more than doubled with respect to previous version (30 profiles available in COSMIC signatures v2), making more critical the associations between signatures and specific mutagenic processes. This study both provides a systematic assessment of the de novo extraction task through simulation scenarios based on the latest version of the COSMIC signatures and highlights, through a novel approach using archetypal analysis, which COSMIC signatures are redundant and more likely to be considered as mathematical artefacts. 29 archetypes were able to reconstruct the profile of all the COSMIC signatures with cosine similarity > 0.8. Interestingly, these archetypes tend to group similar original signatures sharing either the same aetiology or similar biological processes. We believe that these findings will be useful to encourage the development of new de novo extraction methods avoiding the redundancy of information among the signatures while preserving the biological interpretation.
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