1
|
Zhang Y, Li L, Han Q, Wen L. The differential expression of AFF3 in cervical cancer and its correlation with clinicopathological features and prognosis. J OBSTET GYNAECOL 2024; 44:2333784. [PMID: 38602239 DOI: 10.1080/01443615.2024.2333784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/17/2024] [Indexed: 04/12/2024]
Abstract
BACKGROUND Cervical cancer (CC) is the second most common malignancy in women, and identifying biomarkers of CC is crucial for prognosis prediction. Here, we investigated the expression of AF4/FMR2 Family Member 3 (AFF3) in CC and its association with clinicopathological features and prognosis. METHODS Tumour and adjacent tissues, along with clinicopathological features and follow-up information, were collected from 78 patients. AFF3 expression was assessed using quantitative real-time polymerase chain reaction and Western blotting. The correlation between AFF3 expression and CC symptoms was using chi-square test. The 5-year overall survival (OS) was analysed using the Kaplan-Meier method. The Univariate analysis of prognostic risk factors was conducted using the COX proportional hazards model, followed by multivariate COX regression analysis including variables with p < 0.01. RESULTS AFF3 expression was downregulated in CC, and its levels were correlated with lymph node metastasis (LNM) and International Federation of Gynaecology and Obstetrics (FIGO) stage. Patients with low AFF3 expression had a lower 5-year OS rate (52.78%, 19/36). Postoperative survival was reduced in patients with histological grade 3 (G3), myometrial invasion (depth ≥ 1/2), lymphovascular space invasion, LNM, and advanced FIGO stage. Low expression of AFF3 (HR: 2.848, 95% CI: 1.144-7.090) and histological grade G3 (HR: 4.393, 95% CI: 1.663-11.607) were identified as independent prognostic risk factors in CC patients. CONCLUSION Low expression of AFF3 and histological G3 are independent predictors of poor prognosis in CC patients, suggesting that AFF3 could serve as a potential biomarker for prognostic assessment in CC.
Collapse
Affiliation(s)
- Yaxuan Zhang
- Department of Gynaecology and Obstetrics, JiLin Provinc YanBian University Hospital (YanBian Hospital), Yanji City, China
| | - Lanying Li
- Department of Gynecology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou City, China
| | - Qingling Han
- Department of Gynaecology and Obstetrics, JiLin Provinc YanBian University Hospital (YanBian Hospital), Yanji City, China
| | - Lanying Wen
- Department of Gynaecology and Obstetrics, JiLin Provinc YanBian University Hospital (YanBian Hospital), Yanji City, China
| |
Collapse
|
2
|
Aypar U, Dilip D, Gadde R, Londono DM, Liu Y, Gao Q, Geyer MB, Derkach A, Zhang Y, Glass JL, Roshal M, Xiao W. Multilineage involvement in KMT2A-rearranged B acute lymphoblastic leukaemia: cell-of-origin, biology, and clinical implications. Histopathology 2024. [PMID: 38686611 DOI: 10.1111/his.15203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/26/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024]
Abstract
AIMS B lymphoblastic leukaemia/lymphoma (B-ALL) is thought to originate from Pro/Pre-B cells and the genetic aberrations largely reside in lymphoid-committed cells. A recent study demonstrated that a proportion of paediatric B-ALL patients have BCR::ABL1 fusion in myeloid cells, suggesting a chronic myeloid leukaemia (CML)-like biology in this peculiar subset of B-ALL, although it is not entirely clear if the CD19-negative precursor compartment is a source of the myeloid cells. Moreover, the observation has not yet been extended to other fusion-driven B-ALLs. METHODS AND RESULTS In this study we investigated a cohort of KMT2A-rearranged B-ALL patients with a comparison to BCR::ABL1-rearranged B-ALL by performing cell sorting via flow cytometry followed by FISH (fluorescence in situ hybridization) analysis on each of the sorted populations. In addition, RNA sequencing was performed on one of the sorted populations. These analyses showed that (1) multilineage involvement was present in 53% of BCR::ABL1 and 36% of KMT2A-rearranged B-ALL regardless of age, (2) multilineage involvement created pitfalls for residual disease monitoring, and (3) HSPC transcriptome signatures were upregulated in KMT2A-rearranged B-ALL with multilineage involvement. CONCLUSIONS In summary, multilineage involvement is common in both BCR::ABL1-rearranged and KMT2A-rearranged B-ALL, which should be taken into consideration when interpreting the disease burden during the clinical course.
Collapse
Affiliation(s)
- Umut Aypar
- Department of Pathology and Laboratory Medicine, Cytogenetics Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Deepika Dilip
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ramya Gadde
- Department of Pathology and Laboratory Medicine, Hematopathology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dory M Londono
- Department of Pathology and Laboratory Medicine, Cytogenetics Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ying Liu
- Department of Pathology and Laboratory Medicine, Hematopathology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Qi Gao
- Department of Pathology and Laboratory Medicine, Hematopathology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mark B Geyer
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andriy Derkach
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yanming Zhang
- Department of Pathology and Laboratory Medicine, Cytogenetics Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jacob L Glass
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mikhail Roshal
- Department of Pathology and Laboratory Medicine, Hematopathology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wenbin Xiao
- Department of Pathology and Laboratory Medicine, Hematopathology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| |
Collapse
|
3
|
Tirtakusuma R, Milne P, Blair HJ, Shi Y, Bomken S, Heidenreich O. Fusion transcripts are present in early progenitor cells in KMT2A-rearranged B-ALL. Leukemia 2024; 38:883-886. [PMID: 38307942 PMCID: PMC10997500 DOI: 10.1038/s41375-024-02164-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/04/2024]
Affiliation(s)
- Ricky Tirtakusuma
- Wolfson Childhood Cancer Research Centre, Translation and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle Upon Tyne, UK
| | - Paul Milne
- Haematopoiesis and Immunogenomics Laboratory, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, England
| | - Helen J Blair
- Wolfson Childhood Cancer Research Centre, Translation and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle Upon Tyne, UK
| | - Yuzhe Shi
- Center for Cell Engineering and Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Simon Bomken
- Wolfson Childhood Cancer Research Centre, Translation and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle Upon Tyne, UK
| | - Olaf Heidenreich
- Wolfson Childhood Cancer Research Centre, Translation and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle Upon Tyne, UK.
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.
| |
Collapse
|
4
|
Shimony S, Luskin MR. SOHO State of the Art Updates and Next Questions | Approach to Older Adults With Phildadelphia-Chromosome Negative Acute Lymphoblastic Leukemia. Clin Lymphoma Myeloma Leuk 2024; 24:133-140. [PMID: 38102012 DOI: 10.1016/j.clml.2023.10.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 12/17/2023]
Abstract
Philadelphia-chromosome-negative (Ph-neg) acute lymphoblastic leukemia (ALL) has historically been associated with poor outcomes in older patients due to adverse disease biology, as well as inferior tolerance of conventional chemotherapy. Fortunately, novel therapies, including inotuzumab ozogamicin, blinatumomab, and venetoclax, are now being incorporated into first-line therapy to improve efficacy and decrease toxicity of initial therapy. Inotuzumab ozogamicin, alone or in combination with low intensity chemotherapy, appears to be best suited for the induction phase of treatment due to efficacy in the setting of high tumor burden. In contrast, blinatumomab may be best suited for consolidation due to superior efficacy in setting of morphologic remission, with or without measurable residual disease (MRD). Venetoclax is being investigated in combination with chemotherapy and can be used for treatment of older adults with both B-cell and T-cell ALL. Ongoing trials incorporating inotuzumab, blinatumomab, and venetoclax demonstrate high rates of MRD-negative complete remissions with low early mortality. Long-term outcomes have been less favorable so far, with several trials reporting nonrelapse mortality during subsequent treatment. Unanswered questions remain regarding the optimal treatment of older adults with Ph-neg ALL, including central nervous system (CNS) prophylaxis, the most appropriate consolidation to minimize toxicity without compromising efficacy, and the role of transplant and cellular therapy. T-cell ALL remains an area of unmet need and effort is required to ensure that therapeutic advances benefit all populations equitably. In this manuscript, we review current data and ongoing trials regarding the treatment of older adults with Ph-neg ALL and define topics for further research.
Collapse
Affiliation(s)
- Shai Shimony
- Dana-Farber Cancer Institute, Boston, MA; Rabin Medical Center and Faculty of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | | |
Collapse
|
5
|
Ligon JA, Ramakrishna S, Ceppi F, Calkoen FGJ, Diorio C, Davis KL, Jacoby E, Gottschalk S, Schultz LM, Capitini CM. INSPIRED Symposium Part 4B: Chimeric Antigen Receptor T Cell Correlative Studies-Established Findings and Future Priorities. Transplant Cell Ther 2024; 30:155-170. [PMID: 37863355 DOI: 10.1016/j.jtct.2023.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 10/11/2023] [Accepted: 10/13/2023] [Indexed: 10/22/2023]
Abstract
Chimeric antigen receptor (CAR) T cell therapy has revolutionized the treatment of B cell malignancies, with multiple CAR T cell products approved for numerous indications by regulatory agencies worldwide. However, significant work remains to be done to enhance these treatments. In March 2023, a group of experts in CAR T cell therapy assembled at the National Institutes of Health in Bethesda, Maryland at the Insights in Pediatric CAR T Cell Immunotherapy: Recent Advances and Future Directions (INSPIRED) Symposium to identify key areas for research for the coming years. In session 4B, correlative studies to be incorporated into future clinical trials and real-world settings were discussed. Active areas of research identified included (1) optimizing CAR T cell product manufacturing; (2) ensuring adequate lymphodepletion prior to CAR T cell administration; (3) overcoming immunoregulatory cells and tumor stroma present in the tumor microenvironment, particularly in solid tumors; (4) understanding tumor intrinsic properties that lead to CAR T cell immunotherapy resistance; and (5) uncovering biomarkers predictive of treatment resistance, treatment durability, or immune-related adverse events. Here we review the results of previously published clinical trials and real-world studies to summarize what is currently known about each of these topics. We then outline priorities for future research that we believe will be important for improving our understanding of CAR T cell therapy and ultimately leading to better outcomes for patients.
Collapse
Affiliation(s)
- John A Ligon
- Department of Pediatrics, Division of Hematology/Oncology, University of Florida, Gainesville, Florida; University of Florida Health Cancer Center, Gainesville, Florida.
| | - Sneha Ramakrishna
- Stanford Center for Cancer Cell Therapy, Stanford University School of Medicine, Stanford, California; Department of Pediatrics, Stanford University, Stanford, California
| | - Francesco Ceppi
- Division of Pediatrics, Department of Woman-Mother-Child, Pediatric Hematology-Oncology Unit, University Hospital of Lausanne and University of Lausanne, Lausanne, Switzerland
| | - Friso G J Calkoen
- Division of Pediatric Oncology, Princess Maxima Center, Utrecht, The Netherlands
| | - Caroline Diorio
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Kara L Davis
- Stanford Center for Cancer Cell Therapy, Stanford University School of Medicine, Stanford, California; Department of Pediatrics, Stanford University, Stanford, California
| | - Elad Jacoby
- Pediatric Hemato-Oncology, Sheba Medical Center and Tel Aviv University, Tel Aviv, Israel
| | - Stephen Gottschalk
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Liora M Schultz
- Stanford Center for Cancer Cell Therapy, Stanford University School of Medicine, Stanford, California; Department of Pediatrics, Stanford University, Stanford, California
| | - Christian M Capitini
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin; University of Wisconsin Carbone Cancer Center, Madison, Wisconsin
| |
Collapse
|
6
|
Potluri S, Kellaway SG, Coleman DJL, Keane P, Imperato MR, Assi SA, Cockerill PN, Bonifer C. Gene regulation in t(6;9) DEK::NUP214 Acute Myeloid Leukemia resembles that of FLT3-ITD/NPM1 Acute Myeloid Leukemia but with an altered HOX/MEIS axis. Leukemia 2024; 38:403-407. [PMID: 38172329 PMCID: PMC10844093 DOI: 10.1038/s41375-023-02118-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 01/05/2024]
Affiliation(s)
- Sandeep Potluri
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Sophie G Kellaway
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Blood Cancer and Stem Cells, Centre for Cancer Sciences, School of Medicine, University of Nottingham, Nottingham, UK
| | - Daniel J L Coleman
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Peter Keane
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- School of Biosciences, University of Birmingham, Birmingham, UK
| | | | - Salam A Assi
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Peter N Cockerill
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Constanze Bonifer
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK.
| |
Collapse
|
7
|
Bataller A, Abuasab T, McCall D, Wang W, Cuglievan B, Issa GC, Jabbour E, Short N, DiNardo CD, Tang G, Garcia-Manero G, Kantarjian HM, Sasaki K. Myeloid lineage switch in KMT2A-rearranged acute lymphoblastic leukemia treated with lymphoid lineagedirected therapies. Haematologica 2024; 109:293-297. [PMID: 37646654 PMCID: PMC10772528 DOI: 10.3324/haematol.2023.283705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/23/2023] [Indexed: 09/01/2023] Open
Abstract
Not available.
Collapse
Affiliation(s)
- Alex Bataller
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Tareq Abuasab
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - David McCall
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Wei Wang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Branko Cuglievan
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ghayas C Issa
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Elias Jabbour
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Nicholas Short
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Courtney D DiNardo
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Guilin Tang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Hagop M Kantarjian
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Koji Sasaki
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX.
| |
Collapse
|
8
|
Janssens DH, Duran M, Otto DJ, Kirkey D, Yi JS, Meshinchi S, Sarthy JF, Ahmad K, Henikoff S. KMT2A oncoproteins induce epigenetic resistance to targeted therapies. bioRxiv 2023:2023.12.29.573681. [PMID: 38234854 PMCID: PMC10793413 DOI: 10.1101/2023.12.29.573681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Chromosomal translocations involving the Lysine-Methyl-Tansferase-2A ( KMT2A ) locus generate potent oncogenes that cause highly aggressive acute leukemias 1 . KMT2A and the most frequent translocation partners encode proteins that interact with DNA to regulate developmental gene expression 2 . KMT2A-oncogenic fusion proteins (oncoproteins) contribute to the epigenetic mechanisms that allow KMT2A -rearranged leukemias to evade targeted therapies. By profiling the oncoprotein-target sites of 34 KMT2A -rearranged leukemia samples, we find that the genomic enrichment of oncoprotein binding is highly variable between samples. At high levels of expression, the oncoproteins preferentially activate either the lymphoid or myeloid lineage program depending on the fusion partner. These fusion-partner-dependent binding sites correspond to the frequencies of each mutation in acute lymphoid leukemia versus acute myeloid leukemia. By profiling a sample that underwent a lymphoid-to-myeloid lineage switching event in response to lymphoid-directed treatment, we find the global oncoprotein levels are reduced and the oncoprotein-target gene network changes. At lower levels of expression, the oncoprotein shifts to a non-canonical regulatory program that favors the myeloid lineage, and in a subset of resistant patients, the Menin inhibitor Revumenib induces a similar response. The dynamic shifts in KMT2A oncoproteins we describe likely contribute to epigenetic resistance of KMT2A -rearranged leukemias to targeted therapies.
Collapse
|
9
|
Lambo S, Trinh DL, Ries RE, Jin D, Setiadi A, Ng M, Leblanc VG, Loken MR, Brodersen LE, Dai F, Pardo LM, Ma X, Vercauteren SM, Meshinchi S, Marra MA. A longitudinal single-cell atlas of treatment response in pediatric AML. Cancer Cell 2023; 41:2117-2135.e12. [PMID: 37977148 DOI: 10.1016/j.ccell.2023.10.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/15/2023] [Accepted: 10/26/2023] [Indexed: 11/19/2023]
Abstract
Pediatric acute myeloid leukemia (pAML) is characterized by heterogeneous cellular composition, driver alterations and prognosis. Characterization of this heterogeneity and how it affects treatment response remains understudied in pediatric patients. We used single-cell RNA sequencing and single-cell ATAC sequencing to profile 28 patients representing different pAML subtypes at diagnosis, remission and relapse. At diagnosis, cellular composition differed between genetic subgroups. Upon relapse, cellular hierarchies transitioned toward a more primitive state regardless of subtype. Primitive cells in the relapsed tumor were distinct compared to cells at diagnosis, with under-representation of myeloid transcriptional programs and over-representation of other lineage programs. In some patients, this was accompanied by the appearance of a B-lymphoid-like hierarchy. Our data thus reveal the emergence of apparent subtype-specific plasticity upon treatment and inform on potentially targetable processes.
Collapse
Affiliation(s)
- Sander Lambo
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Diane L Trinh
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Rhonda E Ries
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Dan Jin
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Audi Setiadi
- British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada; Department of Pathology & Laboratory Medicine, Division of Hematopathology, Children's and Women's Health Centre of British Columbia, Vancouver, BC, Canada; Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Michelle Ng
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada; Department of Medical Genetics and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Veronique G Leblanc
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | | | | | - Fangyan Dai
- Hematologics, Incorporated, Seattle, WA, USA
| | | | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Suzanne M Vercauteren
- British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada; Department of Pathology & Laboratory Medicine, Division of Hematopathology, Children's and Women's Health Centre of British Columbia, Vancouver, BC, Canada; Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada; Department of Medical Genetics and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada.
| |
Collapse
|
10
|
Iacobucci I, Zeng AGX, Gao Q, Garcia-Prat L, Baviskar P, Shah S, Murison A, Voisin V, Chan-Seng-Yue M, Cheng C, Qu C, Bailey C, Lear M, Witkowski MT, Zhou X, Peraza AZ, Gangwani K, Advani AS, Luger SM, Litzow MR, Rowe JM, Paietta EM, Stock W, Dick JE, Mullighan CG. SINGLE CELL DISSECTION OF DEVELOPMENTAL ORIGINS AND TRANSCRIPTIONAL HETEROGENEITY IN B-CELL ACUTE LYMPHOBLASTIC LEUKEMIA. bioRxiv 2023:2023.12.04.569954. [PMID: 38106088 PMCID: PMC10723356 DOI: 10.1101/2023.12.04.569954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Sequencing of bulk tumor populations has improved genetic classification and risk assessment of B-ALL, but does not directly examine intratumor heterogeneity or infer leukemia cellular origins. We profiled 89 B-ALL samples by single-cell RNA-seq (scRNA-seq) and compared them to a reference map of normal human B-cell development established using both functional and molecular assays. Intra-sample heterogeneity was driven by cell cycle, metabolism, differentiation, and inflammation transcriptional programs. By inference of B lineage developmental state composition, nearly all samples possessed a high abundance of pro-B cells, with variation between samples mainly driven by sub-populations. However, ZNF384- r and DUX4- r B-ALL showed composition enrichment of hematopoietic stem cells, BCR::ABL1 and KMT2A -r ALL of Early Lymphoid progenitors, MEF2D -r and TCF3::PBX1 of Pre-B cells. Enrichment of Early Lymphoid progenitors correlated with high-risk clinical features. Understanding variation in transcriptional programs and developmental states of B-ALL by scRNA-seq refines existing clinical and genomic classifications and improves prediction of treatment outcome.
Collapse
|
11
|
Bueno C, Torres-Ruiz R, Velasco-Hernandez T, Molina O, Petazzi P, Martinez A, Rodriguez V, Vinyoles M, Cantilena S, Williams O, Vega-Garcia N, Rodriguez-Perales S, Segovia JC, Quintana-Bustamante O, Roy A, Meyer C, Marschalek R, Smith AL, Milne TA, Fraga MF, Tejedor JR, Menéndez P. A human genome editing-based MLL::AF4 ALL model recapitulates key cellular and molecular leukemogenic features. Blood 2023; 142:1752-1756. [PMID: 37756522 DOI: 10.1182/blood.2023020858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/20/2023] [Accepted: 08/18/2023] [Indexed: 09/29/2023] Open
Abstract
Cellular ontogeny and MLL breakpoint site influence the capacity of MLL-edited CD34+ hematopoietic cells to initiate and recapitulate infant patients' features in pro-B-cell acute lymphoblastic leukemia (B-ALL). We provide key insights into the leukemogenic determinants of MLL-AF4+ infant B-ALL.
Collapse
Affiliation(s)
- Clara Bueno
- Stem Cell Biology, Immunotherapy and Developmental Leukemia Laboratory. Josep Carreras Leukemia Research Institute, Barcelona, Spain
- Spanish Network for Advanced Therapies, Carlos III Health Institute, Barcelona, Spain
- Spanish Collaborative Cancer Network, Carlos III Health Institute, Barcelona, Spain
| | - Raul Torres-Ruiz
- Stem Cell Biology, Immunotherapy and Developmental Leukemia Laboratory. Josep Carreras Leukemia Research Institute, Barcelona, Spain
- Division of Hematopoietic Innovative Therapies, Biomedical Innovation Unit, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas, Madrid, Spain
- Advanced Therapies Unit, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncologicas, Madrid, Spain
| | - Talia Velasco-Hernandez
- Stem Cell Biology, Immunotherapy and Developmental Leukemia Laboratory. Josep Carreras Leukemia Research Institute, Barcelona, Spain
- Spanish Network for Advanced Therapies, Carlos III Health Institute, Barcelona, Spain
| | - Oscar Molina
- Stem Cell Biology, Immunotherapy and Developmental Leukemia Laboratory. Josep Carreras Leukemia Research Institute, Barcelona, Spain
- Spanish Network for Advanced Therapies, Carlos III Health Institute, Barcelona, Spain
| | - Paolo Petazzi
- Stem Cell Biology, Immunotherapy and Developmental Leukemia Laboratory. Josep Carreras Leukemia Research Institute, Barcelona, Spain
| | - Alba Martinez
- Stem Cell Biology, Immunotherapy and Developmental Leukemia Laboratory. Josep Carreras Leukemia Research Institute, Barcelona, Spain
- Spanish Network for Advanced Therapies, Carlos III Health Institute, Barcelona, Spain
| | - Virginia Rodriguez
- Stem Cell Biology, Immunotherapy and Developmental Leukemia Laboratory. Josep Carreras Leukemia Research Institute, Barcelona, Spain
- Spanish Network for Advanced Therapies, Carlos III Health Institute, Barcelona, Spain
| | - Meritxell Vinyoles
- Stem Cell Biology, Immunotherapy and Developmental Leukemia Laboratory. Josep Carreras Leukemia Research Institute, Barcelona, Spain
- Spanish Network for Advanced Therapies, Carlos III Health Institute, Barcelona, Spain
| | - Sandra Cantilena
- Development Biology Cancer Program, Cancer Section, UCLGOS Institute of Child Health, London, United Kingdom
| | - Owen Williams
- Development Biology Cancer Program, Cancer Section, UCLGOS Institute of Child Health, London, United Kingdom
| | - Nerea Vega-Garcia
- Hematology Laboratory, Hospital Sant Joan de Déu Barcelona, Barcelona, Spain
- Developmental Tumors Biology Group, Leukemia, and other Pediatric Hemopathies, Pediatric Cancer Center Barcelona, Institut de Recerca, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Sandra Rodriguez-Perales
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncologicas, Madrid, Spain
| | - Jose C Segovia
- Division of Hematopoietic Innovative Therapies, Biomedical Innovation Unit, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas, Madrid, Spain
- Advanced Therapies Unit, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
| | - Oscar Quintana-Bustamante
- Division of Hematopoietic Innovative Therapies, Biomedical Innovation Unit, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas, Madrid, Spain
- Advanced Therapies Unit, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
| | - Anindita Roy
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford Biomedical Research Center Hematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
- Department of Pediatrics and National Institute for Health and Care Research Oxford Biomedical Research Centre Hematology Theme, University of Oxford, Oxford, United Kingdom
| | - Claus Meyer
- Diagnostic Center of Acute Leukemia-Institute of Pharmaceutical Biology, Goethe-University, Frankfurt/Main, Germany
| | - Rolf Marschalek
- Diagnostic Center of Acute Leukemia-Institute of Pharmaceutical Biology, Goethe-University, Frankfurt/Main, Germany
| | - Alastair L Smith
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford Biomedical Research Center Hematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Thomas A Milne
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford Biomedical Research Center Hematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Mario F Fraga
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
- Cancer Epigenetics and Nanomedicine Laboratory, Nanomaterials and Nanotechnology Research Center, El Entrego, Spain
- Health Research Institute of Asturias, Institute of Oncology of Asturias and Department of Organisms and Systems Biology, University of Oviedo, Oviedo, Spain
| | - Juan Ramón Tejedor
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
- Cancer Epigenetics and Nanomedicine Laboratory, Nanomaterials and Nanotechnology Research Center, El Entrego, Spain
- Health Research Institute of Asturias, Institute of Oncology of Asturias and Department of Organisms and Systems Biology, University of Oviedo, Oviedo, Spain
| | - Pablo Menéndez
- Stem Cell Biology, Immunotherapy and Developmental Leukemia Laboratory. Josep Carreras Leukemia Research Institute, Barcelona, Spain
- Spanish Network for Advanced Therapies, Carlos III Health Institute, Barcelona, Spain
- Spanish Collaborative Cancer Network, Carlos III Health Institute, Barcelona, Spain
- Department of Biomedicine, University of Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| |
Collapse
|
12
|
Wilson A, Hockney S, Parker J, Angel S, Blair H, Pal D. A human mesenchymal spheroid prototype to replace moderate severity animal procedures in leukaemia drug testing. F1000Res 2023; 11:1280. [PMID: 38046539 PMCID: PMC10691310 DOI: 10.12688/f1000research.123084.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/24/2023] [Indexed: 12/05/2023] Open
Abstract
Patient derived xenograft (PDX) models are regarded as gold standard preclinical models in leukaemia research, especially in testing new drug combinations where typically 45-50 mice are used per assay. 9000 animal experiments are performed annually in the UK in leukaemia research with these expensive procedures being classed as moderate severity, meaning they cause significant pain, suffering and visible distress to animal's state. Furthermore, not all clinical leukaemia samples engraft and when they do data turnaround time can be between 6-12 months. Heavy dependence on animal models is because clinical leukaemia samples do not proliferate in vitro. Alternative cell line models though popular for drug testing are not biomimetic - they are not dependent on the microenvironment for survival, growth and treatment response and being derived from relapse samples they do not capture the molecular complexity observed at disease presentation. Here we have developed an in vitro platform to rapidly establish co-cultures of patient-derived leukaemia cells with 3D bone marrow mesenchyme spheroids, BM-MSC-spheroids. We optimise protocols for developing MSC-spheroid leukaemia co-culture using clinical samples and deliver drug response data within a week. Using three patient samples representing distinct cytogenetics we show that patient-derived-leukaemia cells show enhanced proliferation when co-cultured with MSC-spheroids. In addition, MSC-spheroids provided improved protection against treatment. This makes our spheroids suitable to model treatment resistance - a major hurdle in current day cancer management Given this 3Rs approach is 12 months faster (in delivering clinical data), is a human cell-based biomimetic model and uses 45-50 fewer animals/drug-response assay the anticipated target end-users would include academia and pharmaceutical industry. This animal replacement prototype would facilitate clinically translatable research to be performed with greater ethical, social and financial sustainability.
Collapse
Affiliation(s)
- Aaron Wilson
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, UK, Newcastle upon Tyne, NE1 7RU, UK
| | - Sean Hockney
- Applied Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK
| | - Jessica Parker
- Applied Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK
| | - Sharon Angel
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, UK, Newcastle upon Tyne, NE1 7RU, UK
| | - Helen Blair
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, UK, Newcastle upon Tyne, NE1 7RU, UK
| | - Deepali Pal
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, UK, Newcastle upon Tyne, NE1 7RU, UK
- Applied Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK
| |
Collapse
|
13
|
Sperlazza J, Galeotti J, Hucks G, Alexander TB. Multiple lineage switches in KMT2A rearranged infant leukemia, responsive to combination therapy with CPX-351 and inotuzumab. Pediatr Blood Cancer 2023; 70:e30645. [PMID: 37638847 DOI: 10.1002/pbc.30645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/11/2023] [Accepted: 08/13/2023] [Indexed: 08/29/2023]
Affiliation(s)
- Justin Sperlazza
- Division of Pediatric Hematology-Oncology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Jonathan Galeotti
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - George Hucks
- Division of Pediatric Hematology-Oncology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Thomas B Alexander
- Division of Pediatric Hematology-Oncology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| |
Collapse
|
14
|
Smirnova AO, Miroshnichenkova AM, Belyaeva LD, Kelmanson IV, Lebedev YB, Mamedov IZ, Chudakov DM, Komkov AY. Novel bimodal TRBD1-TRBD2 rearrangements with dual or absent D-region contribute to TRB V-(D)-J combinatorial diversity. Front Immunol 2023; 14:1245175. [PMID: 37744336 PMCID: PMC10513440 DOI: 10.3389/fimmu.2023.1245175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 08/23/2023] [Indexed: 09/26/2023] Open
Abstract
T-cell receptor (TR) diversity of the variable domains is generated by recombination of both the alpha (TRA) and beta (TRB) chains. The textbook process of TRB chain production starts with TRBD and TRBJ gene rearrangement, followed by the rearrangement of a TRBV gene to the partially rearranged D-J gene. Unsuccessful V-D-J TRB rearrangements lead to apoptosis of the cell. Here, we performed deep sequencing of the poorly explored pool of partial TRBD1-TRBD2 rearrangements in T-cell genomic DNA. We reconstructed full repertoires of human partial TRBD1-TRBD2 rearrangements using novel sequencing and validated them by detecting V-D-J recombination-specific byproducts: excision circles containing the recombination signal (RS) joint 5'D2-RS - 3'D1-RS. Identified rearrangements were in compliance with the classical 12/23 rule, common for humans, rats, and mice and contained typical V-D-J recombination footprints. Interestingly, we detected a bimodal distribution of D-D junctions indicating two active recombination sites producing long and short D-D rearrangements. Long TRB D-D rearrangements with two D-regions are coding joints D1-D2 remaining classically on the chromosome. The short TRB D-D rearrangements with no D-region are signal joints, the coding joint D1-D2 being excised from the chromosome. They both contribute to the TRB V-(D)-J combinatorial diversity. Indeed, short D-D rearrangements may be followed by direct V-J2 recombination. Long D-D rearrangements may recombine further with J2 and V genes forming partial D1-D2-J2 and then complete V-D1-D2-J2 rearrangement. Productive TRB V-D1-D2-J2 chains are present and expressed in thousands of clones of human antigen-experienced memory T cells proving their capacity for antigen recognition and actual participation in the immune response.
Collapse
Affiliation(s)
- Anastasia O. Smirnova
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | | | - Laima D. Belyaeva
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Ilya V. Kelmanson
- Department of Biomolecular Sciences and Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Yuri B. Lebedev
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ilgar Z. Mamedov
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Dmitriy M. Chudakov
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Abu Dhabi Stem Cells Center (ADSCC), Abu Dhabi, United Arab Emirates
- Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Alexander Y. Komkov
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Abu Dhabi Stem Cells Center (ADSCC), Abu Dhabi, United Arab Emirates
- Dmitry Rogachev National Medical and Research Center of Pediatric Hematology, Oncology, and Immunology, Moscow, Russia
| |
Collapse
|
15
|
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. Nat 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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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.
| |
Collapse
|
16
|
Abstract
Rapid advances in genomics have opened unprecedented possibilities to explore the mutational landscapes in malignant diseases, such as B-cell acute lymphoblastic leukemia (B-ALL). This disease is manifested as a severe defect in the production of normal blood cells due to the uncontrolled expansion of transformed B-lymphocyte progenitors in the bone marrow. Even though classical genetics identified translocations of transcription factor-coding genes in B-ALL, the extent of the targeting of regulatory networks in malignant transformation was not evident until the emergence of large-scale genomic analyses. There is now evidence that many B-ALL cases present with mutations in genes that encode transcription factors with critical roles in normal B-lymphocyte development. These include PAX5, IKZF1, EBF1, and TCF3, all of which are targeted by translocations or, more commonly, partial inactivation in cases of B-ALL. Even though there is support for the notion that germline polymorphisms in the PAX5 and IKZF1 genes predispose for B-ALL, the majority of leukemias present with somatic mutations in transcription factor-encoding genes. These genetic aberrations are often found in combination with mutations in genes that encode components of the pre-B-cell receptor or the IL-7/TSLP signaling pathways, all of which are important for early B-cell development. This review provides an overview of our current understanding of the molecular interplay that occurs between transcription factors and signaling events during normal and malignant B-lymphocyte development.
Collapse
Affiliation(s)
- Mikael Sigvardsson
- Department of Biomedical and Clinical Sciences, Linköping University, 58185 Linköping, Sweden; Division of Molecular Hematology, Lund University, 22184 Lund, Sweden
| |
Collapse
|
17
|
Lee BM, Summers C, Chisholm KM, Bohling SD, Leger KJ, Gardner R, Annesley C, Lamble AJ. Plasticity of lineage switch in B-ALL allows for successful rechallenge with CD19-directed immunotherapy. Blood Adv 2023; 7:2825-2830. [PMID: 36763522 PMCID: PMC10279539 DOI: 10.1182/bloodadvances.2022009480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/20/2023] [Accepted: 02/04/2023] [Indexed: 02/11/2023] Open
Affiliation(s)
- Brittany M. Lee
- Seattle Children’s Research Institute, Seattle, WA
- Department of Pediatrics, University of Washington School of Medicine, University of Washington, Seattle, WA
| | - Corinne Summers
- Department of Pediatrics, University of Washington School of Medicine, University of Washington, Seattle, WA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Karen M. Chisholm
- Department of Laboratories, Seattle Children’s Hospital, Seattle, WA
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, University of Washington, Seattle, WA
| | - Sandra D. Bohling
- Department of Laboratories, Seattle Children’s Hospital, Seattle, WA
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, University of Washington, Seattle, WA
| | - Kasey J. Leger
- Seattle Children’s Research Institute, Seattle, WA
- Department of Pediatrics, University of Washington School of Medicine, University of Washington, Seattle, WA
| | - Rebecca Gardner
- Seattle Children’s Research Institute, Seattle, WA
- Department of Pediatrics, University of Washington School of Medicine, University of Washington, Seattle, WA
| | - Colleen Annesley
- Seattle Children’s Research Institute, Seattle, WA
- Department of Pediatrics, University of Washington School of Medicine, University of Washington, Seattle, WA
| | - Adam J. Lamble
- Seattle Children’s Research Institute, Seattle, WA
- Department of Pediatrics, University of Washington School of Medicine, University of Washington, Seattle, WA
| |
Collapse
|
18
|
Abstract
Increasing use of chimeric antigen receptor T-cell therapy (CAR-T) has unveiled diverse toxicities warranting specific recognition and management. Cytopenias occurring after CAR-T infusion invariably manifest early (<30 days), commonly are prolonged (30-90 days), and sometimes persist or occur late (>90 days). Variable etiologies of these cytopenias, some of which remain incompletely understood, create clinical conundrums and uncertainties about optimal management strategies. These cytopenias may cause additional sequelae, decreased quality of life, and increased resource use. Early cytopenias are typically attributed to lymphodepletion chemotherapy, however, infections and hyperinflammatory response such as immune effector cell-associated hemophagocytic lymphohistiocytosis-like syndrome may occur. Early and prolonged cytopenias often correlate with severity of cytokine release syndrome or immune effector cell-associated neurotoxicity syndrome. Bone marrow biopsy in patients with prolonged or late cytopenias is important to evaluate for primary disease and secondary marrow neoplasm in both pediatric and adult patients. Commonly, cytopenias resolve over time and evidence for effective interventions is often anecdotal. Treatment strategies, which are limited and require tailoring based upon likely underlying etiology, include growth factors, thrombopoietin-receptor agonist, stem cell boost, transfusion support, and abrogation of infection risk. Here we provide our approach, including workup and management strategies, for cytopenias after CAR-T.
Collapse
Affiliation(s)
- Tania Jain
- Division of Hematological Malignancies and Bone Marrow Transplantation, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD
| | - Timothy S. Olson
- Department of Pediatrics, Children’s Hospital of Philadelphia, Perelman School of Medicine at The University of Pennsylvania, Philadelphia, PA
| | - Frederick L. Locke
- Department of Blood and Marrow Transplant and Cellular Immunotherapy, Moffitt Cancer Center, Tampa, FL
| |
Collapse
|
19
|
Külp M, Larghero P, Alten J, Cario G, Eckert C, Caye-Eude A, Cavé H, Schmachtel T, Bardini M, Cazzaniga G, De Lorenzo P, Valsecchi MG, Bonig H, Meyer C, Rieger MA, Marschalek R. The EGR3 regulome of infant KMT2A-r acute lymphoblastic leukemia identifies differential expression of B-lineage genes predictive for outcome. Leukemia 2023:10.1038/s41375-023-01895-z. [PMID: 37100882 PMCID: PMC10132433 DOI: 10.1038/s41375-023-01895-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/28/2023] [Accepted: 03/31/2023] [Indexed: 04/28/2023]
Abstract
KMT2A-rearranged acute lymphoblastic infant leukemia (KMT2A-r iALL) is associated with outsize risk of relapse and relapse mortality. We previously reported strong upregulation of the immediate early gene EGR3 in KMT2A::AFF1 iALL at relapse; now we provide analyses of the EGR3 regulome, which we assessed through binding and expression target analysis of an EGR3-overexpressing t(4;11) cell culture model. Our data identify EGR3 as a regulator of early B-lineage commitment. Principal component analysis of 50 KMT2A-r iALL patients at diagnosis and 18 at relapse provided strictly dichotomous separation of patients based on the expression of four B-lineage genes. Absence of B-lineage gene expression translates to more than two-fold poorer long-term event-free survival. In conclusion, our study presents four B-lineage genes with prognostic significance, suitable for gene expression-based risk stratification of KMT2A-r iALL patients.
Collapse
Affiliation(s)
- Marius Külp
- Diagnostic Center of Acute Leukemia (DCAL), Institute of Pharmaceutical Biology, Goethe-University, Frankfurt am Main, Germany.
- Department of Medicine, Hematology/Oncology, Goethe University Hospital Frankfurt, Frankfurt am Main, Germany.
| | - Patrizia Larghero
- Diagnostic Center of Acute Leukemia (DCAL), Institute of Pharmaceutical Biology, Goethe-University, Frankfurt am Main, Germany
| | - Julia Alten
- Department of Pediatrics, University Medical Center Schleswig-Holstein, Campus Kiel, Germany
| | - Gunnar Cario
- Department of Pediatrics, University Medical Center Schleswig-Holstein, Campus Kiel, Germany
| | - Cornelia Eckert
- Department of Pediatric Hematology and Oncology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Aurélie Caye-Eude
- Genetics Department, AP-HP, Hôpital Robert Debré, F-75019, Paris, France
- Université Paris Cité, Inserm U1131, Institut de recherche Saint-Louis, F-75010, Paris, France
| | - Hélène Cavé
- Genetics Department, AP-HP, Hôpital Robert Debré, F-75019, Paris, France
- Université Paris Cité, Inserm U1131, Institut de recherche Saint-Louis, F-75010, Paris, France
| | - Tessa Schmachtel
- Department of Medicine, Hematology/Oncology, Goethe University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Michela Bardini
- Centro Ricerca Tettamanti, Pediatrics, University of Milan-Bicocca, Fondazione Monza e Brianza per il Bambino e la sua Mamma (MBBM)/San Gerardo Hospital, Monza, Italy
| | - Giovanni Cazzaniga
- Centro Ricerca Tettamanti, Pediatrics, University of Milan-Bicocca, Fondazione Monza e Brianza per il Bambino e la sua Mamma (MBBM)/San Gerardo Hospital, Monza, Italy
- Genetics, School of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
| | - Paola De Lorenzo
- Statistical Section, Pediatric Clinic, University of Milan-Bicocca, Monza, Italy
| | - Maria Grazia Valsecchi
- Center of Bioinformatics, Biostatistics and Bioimaging, University of Milan-Bicocca, Monza, Italy
| | - Halvard Bonig
- Institute for Transfusion Medicine and Immunohematology, Goethe University, Frankfurt am Main, Germany
- German Red Cross Blood Service Baden-Württemberg-Hessen, Frankfurt am Main, Germany
- Department of Medicine, Division of Hematology, University of Washington School of Medicine, Seattle, WA, USA
| | - Claus Meyer
- Diagnostic Center of Acute Leukemia (DCAL), Institute of Pharmaceutical Biology, Goethe-University, Frankfurt am Main, Germany
| | - Michael A Rieger
- Department of Medicine, Hematology/Oncology, Goethe University Hospital Frankfurt, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKZF), Heidelberg, Germany
- Cardio-Pulmonary Institute, Frankfurt am Main, Germany
| | - Rolf Marschalek
- Diagnostic Center of Acute Leukemia (DCAL), Institute of Pharmaceutical Biology, Goethe-University, Frankfurt am Main, Germany.
| |
Collapse
|
20
|
Goodlad JR, Xiao W, Amador C, Cook JR, Happ L, Thakkar D, Dave S, Dogan A, Duffield A, Nejati R, Ott G, Wasik M, Czader M. Phenotypic and genotypic infidelity in B-lineage neoplasms, including transdifferentiation following targeted therapy: Report from the 2021 SH/EAHP Workshop. Am J Clin Pathol 2023:7135991. [PMID: 37085149 DOI: 10.1093/ajcp/aqad035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 03/13/2023] [Indexed: 04/23/2023] Open
Abstract
OBJECTIVES Session 2 of the 2021 Society for Hematopathology and European Association for Haematopathology Workshop collected examples of lineage infidelity and transdifferentiation in B-lineage neoplasms, including after targeted therapy. METHODS Twenty cases were submitted. Whole-exome sequencing and genome-wide RNA expression analysis were available on a limited subsample. RESULTS A diagnosis of B-cell acute lymphoblastic leukemia (B-ALL) was rendered on at least 1 biopsy from 13 patients. There was 1 case of acute myeloid leukemia (AML); the remaining 6 cases were mature B-cell neoplasms. Targeted therapy was administered in 7 cases of B-ALL and 4 cases of mature B-cell neoplasms. Six cases of B-ALL underwent lineage switch to AML or mixed-phenotype acute leukemia at relapse, 5 of which had rearranged KMT2A. Changes in maturational state without lineage switch were observed in 2 cases. Examples of de novo aberrant T-cell antigen expression (n = 2) were seen among the mature B-cell lymphoma cohort, and their presence correlated with alterations in tumor cell gene expression patterns. CONCLUSIONS This cohort of cases enabled us to illustrate, discuss, and review current concepts of lineage switch and aberrant antigen expression in a variety of B-cell neoplasms and draw attention to the role targeted therapies may have in predisposing neoplasms to transdifferentiation as well as other, less expected changes in maturational status.
Collapse
Affiliation(s)
- John R Goodlad
- Department of Pathology, NHS Greater Glasgow and Clyde, Glasgow, UK
| | - Wenbin Xiao
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, US
| | - Catalina Amador
- Department of Pathology and Laboratory Medicine, University of Miami Miller School of Medicine, Miami, FL, US
| | - James R Cook
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, OH, US
| | | | | | - Sandeep Dave
- Center for Genomic and Computational Biology and Department of Medicine, Duke University School of Medicine, Durham, NC, US
| | - Ahmet Dogan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, US
| | - Amy Duffield
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, US
| | - Reza Nejati
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA, US
| | - German Ott
- Department of Clinical Pathology, Robert-Bosch-Krankenhaus, and Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
| | - Mariusz Wasik
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA, US
| | - Magdalena Czader
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, US
| |
Collapse
|
21
|
Smirnova AO, Miroshnichenkova AM, Olshanskaya YV, Maschan MA, Lebedev YB, Chudakov DM, Mamedov IZ, Komkov A. The use of non-functional clonotypes as a natural calibrator for quantitative bias correction in adaptive immune receptor repertoire profiling. eLife 2023; 12:69157. [PMID: 36692004 PMCID: PMC9901932 DOI: 10.7554/elife.69157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 01/22/2023] [Indexed: 01/25/2023] Open
Abstract
High-throughput sequencing of adaptive immune receptor repertoires is a valuable tool for receiving insights in adaptive immunity studies. Several powerful TCR/BCR repertoire reconstruction and analysis methods have been developed in the past decade. However, detecting and correcting the discrepancy between real and experimentally observed lymphocyte clone frequencies are still challenging. Here, we discovered a hallmark anomaly in the ratio between read count and clone count-based frequencies of non-functional clonotypes in multiplex PCR-based immune repertoires. Calculating this anomaly, we formulated a quantitative measure of V- and J-genes frequency bias driven by multiplex PCR during library preparation called Over Amplification Rate (OAR). Based on the OAR concept, we developed an original software for multiplex PCR-specific bias evaluation and correction named iROAR: immune Repertoire Over Amplification Removal (https://github.com/smiranast/iROAR). The iROAR algorithm was successfully tested on previously published TCR repertoires obtained using both 5' RACE (Rapid Amplification of cDNA Ends)-based and multiplex PCR-based approaches and compared with a biological spike-in-based method for PCR bias evaluation. The developed approach can increase the accuracy and consistency of repertoires reconstructed by different methods making them more applicable for comparative analysis.
Collapse
Affiliation(s)
- Anastasia O Smirnova
- Skolkovo Institute of Science and TechnologyMoscowRussian Federation
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
| | - Anna M Miroshnichenkova
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and ImmunologyMoscowRussian Federation
| | - Yulia V Olshanskaya
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and ImmunologyMoscowRussian Federation
| | - Michael A Maschan
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and ImmunologyMoscowRussian Federation
| | - Yuri B Lebedev
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Pirogov Russian National Research Medical UniversityMoscowRussian Federation
| | - Dmitriy M Chudakov
- Skolkovo Institute of Science and TechnologyMoscowRussian Federation
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Pirogov Russian National Research Medical UniversityMoscowRussian Federation
- Abu Dhabi Stem Cells CenterAbu DhabiUnited Arab Emirates
| | - Ilgar Z Mamedov
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Pirogov Russian National Research Medical UniversityMoscowRussian Federation
| | - Alexander Komkov
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and ImmunologyMoscowRussian Federation
| |
Collapse
|
22
|
|
23
|
Shi Q, Han S, Liu X, Wang S, Ma H. Integrated single-cell and transcriptome sequencing analyses determines a chromatin regulator-based signature for evaluating prognosis in lung adenocarcinoma. Front Oncol 2022; 12:1031728. [PMID: 36324565 PMCID: PMC9618736 DOI: 10.3389/fonc.2022.1031728] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 09/28/2022] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND Accumulating evidence has highlighted the significance of chromatin regulator (CR) in pathogenesis and progression of cancer. However, the prognostic role of CRs in LUAD remains obscure. We aim to detect the prognostic value of CRs in LUAD and create favorable signature for assessing prognosis and clinical value of LUAD patients. METHODS The mRNA sequencing data and clinical information were obtained from TCGA and GEO databases. Gene consensus clustering analysis was utilized to determine the molecular subtype of LUAD. Cox regression methods were employed to set up the CRs-based signature (CRBS) for evaluating survival rate in LUAD. Biological function and signaling pathways were identified by KEGG and GSEA analyses. In addition, we calculated the infiltration level of immunocyte by CIBERSORT algorithm. The expressions of model hub genes were detected in LUAD cell lines by real-time polymerase chain reaction (PCR). RESULTS KEGG analysis suggested the CRs were mainly involved in histone modification, nuclear division and DNA modification. Consensus clustering analysis identified a novel CRs-associated subtype which divided the combined LUAD cohort into two clusters (C1 = 217 and C2 = 296). We noticed that a remarkable discrepancy in survival rate among two clusters. Then, a total of 120 differentially expressed CRs were enrolled into stepwise Cox analyses. Four hub CRs (CBX7, HMGA2, NPAS2 and PRC1) were selected to create a risk signature which could accurately forecast patient outcomes and differentiate patient risk. GSEA unearthed that mTORC1 pathway, PI3K/Akt/mTOR and p53 pathway were greatly enriched in CRBS-high cohort. Moreover, the infiltration percentages of macrophage M0, macrophage M2, resting NK cells, memory B cells, dendritic cells and mast cells were statistically significantly different in the two groups. PCR assay confirmed the differential expression of four model biomarkers. CONCLUSIONS Altogether, our project developed a robust risk signature based on CRs and offered novel insights into individualized treatment for LUAD cases.
Collapse
Affiliation(s)
- Qingtong Shi
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
- Department of Thoracic Surgery, The Affiliated Hospital of Yangzhou University, Yangzhou, China
| | - Song Han
- Department of Thoracic Surgery, Suzhou Science and Technology Town Hospital, Suzhou, China
| | - Xiong Liu
- Department of Thoracic Surgery, The Affiliated Hospital of Yangzhou University, Yangzhou, China
- Graduate School of Dalian Medical University, Dalian, China
| | - Saijian Wang
- Department of Thoracic Surgery, The Affiliated Hospital of Yangzhou University, Yangzhou, China
- Graduate School of Dalian Medical University, Dalian, China
| | - Haitao Ma
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| |
Collapse
|
24
|
Liu Z, Zhou Z, Dang Q, Xu H, Lv J, Li H, Han X. Immunosuppression in tumor immune microenvironment and its optimization from CAR-T cell therapy. Am J Cancer Res 2022; 12:6273-6290. [PMID: 36168626 PMCID: PMC9475465 DOI: 10.7150/thno.76854] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/17/2022] [Indexed: 11/17/2022] Open
Abstract
Chimeric antigen receptor (CAR)-T cell therapy represents a landmark advance in personalized cancer treatment. CAR-T strategy generally engineers T cells from a specific patient with a new antigen-specificity, which has achieved considerable success in hematological malignancies, but scarce benefits in solid tumors. Recent studies have demonstrated that tumor immune microenvironment (TIME) cast a profound impact on the immunotherapeutic response. The immunosuppressive landscape of TIME is a critical obstacle to the effector activity of CAR-T cells. Nevertheless, every cloud has a silver lining. The immunosuppressive components also shed new inspiration on reshaping a friendly TIME by targeting them with engineered CARs. Herein, we summarize recent advances in disincentives of TIME and discuss approaches and technologies to enhance CAR-T cell efficacy via addressing current hindrances. Simultaneously, we firmly believe that by parsing the immunosuppressive components of TIME, rationally manipulating the complex interactions of immunosuppressive components, and optimizing CAR-T cell therapy for each patient, the CAR-T cell immunotherapy responsiveness for solid malignancies will be substantially enhanced, and novel therapeutic targets will be revealed.
Collapse
Affiliation(s)
- Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China.,Interventional Institute of Zhengzhou University, Zhengzhou, Henan 450052, China.,Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, Henan 450052, China
| | - Zhaokai Zhou
- Department of Pediatric Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Qin Dang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Hui Xu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Jinxiang Lv
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Huanyun Li
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China.,Interventional Institute of Zhengzhou University, Zhengzhou, Henan 450052, China.,Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, Henan 450052, China
| |
Collapse
|