Andrew W Allbee, James Gerson, Guang Yang, Adam Bagg
{"title":"PD-L1<sup>+</sup> diffuse large B-cell lymphoma with extremely high mutational burden and microsatellite instability due to acquired <i>PMS2</i> mutation.","authors":"Andrew W Allbee, James Gerson, Guang Yang, Adam Bagg","doi":"10.1101/mcs.a006318","DOIUrl":"10.1101/mcs.a006318","url":null,"abstract":"<p><p>We present a unique case of a single patient presenting with two mutationally distinct, PD-L1<sup>+</sup> diffuse large B-cell lymphomas (DLBCLs). One of these DLBCLs demonstrated exceptionally high mutational burden (eight disease-associated variants and 41 variants of undetermined significance) with microsatellite instability (MSI) and an acquired <i>PMS2</i> mutation with loss of PMS2 protein expression, detected postchemotherapy. This report, while highlighting the extent of possible tumor heterogeneity across separate clonal expansions as well as possible syndromic B-cell neoplasia, supports the notion that, although rare, PD-L1 expression and associated states permissive of high mutational burden (such as mismatch repair gene loss of function/MSI) should be more routinely considered in DLBCLs. Appropriate testing may be predictive of outcome and inform the utility of targeted therapy in these genetically diverse and historically treatment-refractory malignancies.</p>","PeriodicalId":10360,"journal":{"name":"Cold Spring Harbor Molecular Case Studies","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10815288/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139416551","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Lea Abou Haidar, Robert C Harris, Panayotis Pachnis, Hongli Chen, Garrett K Gotway, Min Ni, Ralph J DeBerardinis
{"title":"Novel pathogenic <i>UQCRC2</i> variants in a female with normal neurodevelopment.","authors":"Lea Abou Haidar, Robert C Harris, Panayotis Pachnis, Hongli Chen, Garrett K Gotway, Min Ni, Ralph J DeBerardinis","doi":"10.1101/mcs.a006295","DOIUrl":"10.1101/mcs.a006295","url":null,"abstract":"<p><p>Electron transport chain (ETC) disorders are a group of rare, multisystem diseases caused by impaired oxidative phosphorylation and energy production. Deficiencies in complex III (CIII), also known as ubiquinol-cytochrome <i>c</i> reductase, are particularly rare in humans. Ubiquinol-cytochrome <i>c</i> reductase core protein 2 (<i>UQCRC2</i>) encodes a subunit of CIII that plays a crucial role in dimerization. Several pathogenic <i>UQCRC2</i> variants have been identified in patients presenting with metabolic abnormalities that include lactic acidosis, hyperammonemia, hypoglycemia, and organic aciduria. Almost all previously reported <i>UQCRC2</i>-deficient patients exhibited neurodevelopmental involvement, including developmental delays and structural brain anomalies. Here, we describe a girl who presented at 3 yr of age with lactic acidosis, hyperammonemia, and hypoglycemia but has not shown any evidence of neurodevelopmental dysfunction by age 15. Whole-exome sequencing revealed compound heterozygosity for two novel variants in <i>UQCRC2</i>: c.1189G>A; p.Gly397Arg and c.437T>C; p.Phe146Ser. Here, we discuss the patient's clinical presentation and the likely pathogenicity of these two missense variants.</p>","PeriodicalId":10360,"journal":{"name":"Cold Spring Harbor Molecular Case Studies","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10815277/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10234223","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Dingani Nkosi, Andrew W Allbee, Paul G Rothberg, Jonathan W Friedberg, Andrew G Evans
{"title":"Common clonal origin of three distinct hematopoietic neoplasms in a single patient: B-cell lymphoma, T-cell lymphoma, and polycythemia vera.","authors":"Dingani Nkosi, Andrew W Allbee, Paul G Rothberg, Jonathan W Friedberg, Andrew G Evans","doi":"10.1101/mcs.a006313","DOIUrl":"10.1101/mcs.a006313","url":null,"abstract":"<p><p>The potential for more than one distinct hematolymphoid neoplasm to arise from a common mutated stem or precursor cell has been proposed based on findings in primary human malignancies. Particularly, angioimmunoblastic T-cell lymphoma (AITL), which shares a somatic mutation profile in common with other hematopoietic malignancies, has been reported to occur alongside myeloid neoplasms or clonal B-cell proliferations, with identical mutations occurring in more than one cell lineage. Here we report such a case of an elderly woman who was diagnosed over a period of 8 years with diffuse large B-cell lymphoma, polycythemia vera, and AITL, each harboring identical somatic mutations in multiple genes. Overall, at least five identical nucleotide mutations were shared across multiple specimens, with two identical mutations co-occurring at variable variant allele frequencies in all three specimen types. These findings lend credence to the theory that a common mutated stem cell could give rise to multiple neoplasms through parallel hematopoietic differentiation pathways.</p>","PeriodicalId":10360,"journal":{"name":"Cold Spring Harbor Molecular Case Studies","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10815289/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139416550","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jagadish Chandrabose Sundaramurthi, Anita M Bagley, Hannah Blau, Leigh Carmody, Amy Crandall, Daniel Danis, Michael A Gargano, Anxhela Gjyshi Gustafson, Ellen M Raney, Mallory Shingle, Jon R Davids, Peter N Robinson
{"title":"De novo <i>TRPM3</i> missense variant associated with neurodevelopmental delay and manifestations of cerebral palsy.","authors":"Jagadish Chandrabose Sundaramurthi, Anita M Bagley, Hannah Blau, Leigh Carmody, Amy Crandall, Daniel Danis, Michael A Gargano, Anxhela Gjyshi Gustafson, Ellen M Raney, Mallory Shingle, Jon R Davids, Peter N Robinson","doi":"10.1101/mcs.a006293","DOIUrl":"10.1101/mcs.a006293","url":null,"abstract":"<p><p>We identified a de novo heterozygous transient receptor potential cation channel subfamily M (melastatin) member 3 (<i>TRPM3</i>) missense variant, p.(Asn1126Asp), in a patient with developmental delay and manifestations of cerebral palsy (CP) using phenotype-driven prioritization analysis of whole-genome sequencing data with Exomiser. The variant is localized in the functionally important ion transport domain of the TRPM3 protein and predicted to impact the protein structure. Our report adds <i>TRPM3</i> to the list of Mendelian disease-associated genes that can be associated with CP and provides further evidence for the pathogenicity of the variant p.(Asn1126Asp).</p>","PeriodicalId":10360,"journal":{"name":"Cold Spring Harbor Molecular Case Studies","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10815282/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10557473","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Swetha Ramadesikan, Caitlyn M Colwell, Rachel Supinger, Jesse Hunter, Jessica Thomas, Elizabeth Varga, Elaine R Mardis, Richard J Wood, Daniel C Koboldt
{"title":"Novel inherited <i>CDX2</i> variant segregating in a family with diverse congenital malformations of the genitourinary system.","authors":"Swetha Ramadesikan, Caitlyn M Colwell, Rachel Supinger, Jesse Hunter, Jessica Thomas, Elizabeth Varga, Elaine R Mardis, Richard J Wood, Daniel C Koboldt","doi":"10.1101/mcs.a006294","DOIUrl":"10.1101/mcs.a006294","url":null,"abstract":"<p><p>Anorectal malformations (ARMs) constitute a group of congenital defects of the gastrointestinal and urogenital systems. They affect males and females, with an estimated worldwide prevalence of 1 in 5000 live births. These malformations are clinically heterogeneous and can be part of a syndromic presentation (syndromic ARM) or as a nonsyndromic entity (nonsyndromic ARM). Despite the well-recognized heritability of nonsyndromic ARM, the genetic etiology in most patients is unknown. In this study, we describe three siblings with diverse congenital anomalies of the genitourinary system, anemia, delayed milestones, and skeletal anomalies. Genome sequencing identified a novel, paternally inherited heterozygous Caudal type Homeobox 2 (<i>CDX2</i>) variant (c.722A > G (p.Glu241Gly)), that was present in all three affected siblings. The variant identified in this family is absent from population databases and predicted to be damaging by most in silico pathogenicity tools. So far, only two other reports implicate variants in <i>CDX2</i> with ARMs. Remarkably, the individuals described in these studies had similar clinical phenotypes and genetic alterations in <i>CDX2</i> <i>CDX2</i> encodes a transcription factor and is considered the master regulator of gastrointestinal development. This variant maps to the homeobox domain of the encoded protein, which is critical for interaction with DNA targets. Our finding provides a potential molecular diagnosis for this family's condition and supports the role of <i>CDX2</i> in anorectal anomalies. It also highlights the clinical heterogeneity and variable penetrance of ARM predisposition variants, another well-documented phenomenon. Finally, it underscores the diagnostic utility of genomic profiling of ARMs to identify the genetic etiology of these defects.</p>","PeriodicalId":10360,"journal":{"name":"Cold Spring Harbor Molecular Case Studies","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10815271/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41193559","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pauline Tibout, Joel Livingston, Nisha Kanwar, Kyoko E Yuki, Adam Shlien, Bo Ngan, Meredith S Irwin, Daniel A Morgenstern, Johann Hitzler, Anita Villani, Sarah Cohen-Gogo
{"title":"Synchronous T-lymphoblastic lymphoma and neuroblastoma in a 3-yr-old with novel germline <i>SMARCA4</i> and <i>EZH2</i> variants.","authors":"Pauline Tibout, Joel Livingston, Nisha Kanwar, Kyoko E Yuki, Adam Shlien, Bo Ngan, Meredith S Irwin, Daniel A Morgenstern, Johann Hitzler, Anita Villani, Sarah Cohen-Gogo","doi":"10.1101/mcs.a006286","DOIUrl":"10.1101/mcs.a006286","url":null,"abstract":"<p><p>T-lymphoblastic lymphoma (T-LLy) is the most common lymphoblastic lymphoma in children and often presents with a mediastinal mass. Lymphomatous suprarenal masses are possible but rare. Here, we discuss the case of a previously healthy 3-yr-old male who presented with mediastinal T-LLy with bilateral suprarenal masses. Following initial treatment, surgical biopsy of persisting adrenal masses revealed bilateral neuroblastoma (NBL). A clinical genetics panel for germline cancer predisposition did not identify any pathogenic variants. Combination large panel (864 genes) profiling analysis in the context of a precision oncology study revealed two novel likely pathogenic heterozygous variants: <i>SMARCA4</i> c.1420-1G > T p.? and <i>EZH2</i> c.1943G > C p.(Ile631Phefs*44). Somatic analysis revealed potential second hits/somatic variants in <i>EZH2</i> (in the T-LLy) and a segmental loss in Chromosome 19p encompassing <i>SMARCA4</i> (in the NBL). Synchronous cancers, especially at a young age, warrant genetic evaluation for cancer predisposition; enrollment in a precision oncology program assessing germline and tumor DNA can fulfill that purpose, particularly when standard first-line genetic testing is negative and in the setting of tumors that are not classic for common cancer predisposition syndromes.</p>","PeriodicalId":10360,"journal":{"name":"Cold Spring Harbor Molecular Case Studies","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10815281/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71478774","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Kyle M Hernandez, Aarti Venkat, Danne C Elbers, John R Bihn, Mary T Brophy, Nhan V Do, Jennifer La, Qiong Liu, Andrew Prokhorenkov, Noah Metoki-Shlubsky, Feng-Chi Sung, Channing J Paller, Nathanael R Fillmore, Robert L Grossman
{"title":"Prostate cancer patient stratification by molecular signatures in the Veterans Precision Oncology Data Commons.","authors":"Kyle M Hernandez, Aarti Venkat, Danne C Elbers, John R Bihn, Mary T Brophy, Nhan V Do, Jennifer La, Qiong Liu, Andrew Prokhorenkov, Noah Metoki-Shlubsky, Feng-Chi Sung, Channing J Paller, Nathanael R Fillmore, Robert L Grossman","doi":"10.1101/mcs.a006298","DOIUrl":"10.1101/mcs.a006298","url":null,"abstract":"<p><p>Veterans are at an increased risk for prostate cancer, a disease with extraordinary clinical and molecular heterogeneity, compared with the general population. However, little is known about the underlying molecular heterogeneity within the veteran population and its impact on patient management and treatment. Using clinical and targeted tumor sequencing data from the National Veterans Affairs health system, we conducted a retrospective cohort study on 45 patients with advanced prostate cancer in the Veterans Precision Oncology Data Commons (VPODC), most of whom were metastatic castration-resistant. We characterized the mutational burden in this cohort and conducted unsupervised clustering analysis to stratify patients by molecular alterations. Veterans with prostate cancer exhibited a mutational landscape broadly similar to prior studies, including <i>KMT2A</i> and <i>NOTCH1</i> mutations associated with neuroendocrine prostate cancer phenotype, previously reported to be enriched in veterans. We also identified several potential novel mutations in <i>PTEN</i>, <i>MSH6</i>, <i>VHL</i>, <i>SMO</i>, and <i>ABL1</i> Hierarchical clustering analysis revealed two subgroups containing therapeutically targetable molecular features with novel mutational signatures distinct from those reported in the Catalogue of Somatic Mutations in Cancer database. The clustering approach presented in this study can potentially be used to clinically stratify patients based on their distinct mutational profiles and identify actionable somatic mutations for precision oncology.</p>","PeriodicalId":10360,"journal":{"name":"Cold Spring Harbor Molecular Case Studies","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10815278/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138482093","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The diagnostic odyssey of a patient with dihydropyrimidinase deficiency: a case report and review of the literature.","authors":"Daniah Albokhari, Ohood Alharbi, Alyssa Blesson, Mahim Jain","doi":"10.1101/mcs.a006319","DOIUrl":"10.1101/mcs.a006319","url":null,"abstract":"<p><p>Dihydropyrimidinase (DHP) deficiency is an autosomal recessive metabolic disorder caused by biallelic pathogenic variants of <i>DPYS</i> Patients with DHP deficiency exhibit a broad spectrum of phenotypes, ranging from severe neurological and gastrointestinal involvement to cases with no apparent symptoms. The biochemical diagnosis of DHP deficiency is based on the detection of a significant amount of dihydropyrimidines in urine, plasma, and cerebrospinal fluid samples. Molecular genetic testing, specifically the identification of biallelic pathogenic variants in <i>DPYS</i>, has proven instrumental in confirming the diagnosis and facilitating family studies. This case study documents the diagnostic journey of an 18-yr-old patient with DHP deficiency, highlighting features at the severe end of the clinical spectrum. Notably, our patient exhibited previously unreported skeletal features that positively responded to bisphosphonate treatment, contributing valuable insights to the clinical characterization of DHP deficiency. Additionally, a novel <i>DPYS</i> variant was identified and confirmed pathogenicity through metabolic testing, further expanding the variant spectrum of the gene. Our case emphasizes the importance of a comprehensive diagnostic approach using genetic sequencing and metabolic testing for accurate diagnosis.</p>","PeriodicalId":10360,"journal":{"name":"Cold Spring Harbor Molecular Case Studies","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10815279/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139416552","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Majd Al Assaad, Gunes Gundem, Benjamin Liechty, Andrea Sboner, Juan Medina, Elli Papaemmanuil, Cora N Sternberg, Asher Marks, Mark M Souweidane, Jeffrey P Greenfield, Ivy Tran, Matija Snuderl, Olivier Elemento, Marcin Imielinski, David J Pisapia, Juan Miguel Mosquera
{"title":"The importance of escalating molecular diagnostics in patients with low-grade pediatric brain cancer.","authors":"Majd Al Assaad, Gunes Gundem, Benjamin Liechty, Andrea Sboner, Juan Medina, Elli Papaemmanuil, Cora N Sternberg, Asher Marks, Mark M Souweidane, Jeffrey P Greenfield, Ivy Tran, Matija Snuderl, Olivier Elemento, Marcin Imielinski, David J Pisapia, Juan Miguel Mosquera","doi":"10.1101/mcs.a006275","DOIUrl":"10.1101/mcs.a006275","url":null,"abstract":"<p><p>Pilocytic astrocytomas are the most common pediatric brain tumors, typically presenting as low-grade neoplasms. We report two cases of pilocytic astrocytoma with atypical tumor progression. Case 1 involves a 12-yr-old boy with an unresectable suprasellar tumor, negative for <i>BRAF</i> rearrangement but harboring a <i>BRAF</i> p.V600E mutation. He experienced tumor size reduction and stable disease following dabrafenib treatment. Case 2 describes a 6-yr-old boy with a thalamic tumor that underwent multiple resections, with no actionable driver detected using targeted next-generation sequencing. Whole-genome and RNA-seq analysis identified an internal tandem duplication in <i>FGFR1</i> and RAS pathway activation. Future management options include FGFR1 inhibitors. These cases demonstrate the importance of escalating molecular diagnostics for pediatric brain cancer, advocating for early reflexing to integrative whole-genome sequencing and transcriptomic profiling when targeted panels are uninformative. Identifying molecular drivers can significantly impact treatment decisions and improve patient outcomes.</p>","PeriodicalId":10360,"journal":{"name":"Cold Spring Harbor Molecular Case Studies","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10815291/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10129379","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Patricia M Kim, Reza Nejati, Pin Lu, Devang Thakkar, Nicholas Mackrides, Vanessa Dupoux, Shazia Nakhoda, Don A Baldwin, Jianming Pei, Sandeep S Dave, Y Lynn Wang, Mariusz A Wasik
{"title":"Leukemic presentation and progressive genomic alterations of MCD/C5 diffuse large B-cell lymphoma (DLBCL).","authors":"Patricia M Kim, Reza Nejati, Pin Lu, Devang Thakkar, Nicholas Mackrides, Vanessa Dupoux, Shazia Nakhoda, Don A Baldwin, Jianming Pei, Sandeep S Dave, Y Lynn Wang, Mariusz A Wasik","doi":"10.1101/mcs.a006283","DOIUrl":"10.1101/mcs.a006283","url":null,"abstract":"<p><p>Diffuse large B-cell lymphoma (DLBCL) is a heterogenous group of lymphoid malignancies. Based on gene expression profiling, it has been subdivided into germinal center (GC)-derived and activated B-cell (ABC) types. Advances in molecular methodologies have further refined the subclassification of DLBCL, based on recurrent genetic abnormalities. Here, we describe a distinct case of DLBCL that presented in leukemic form. DNA sequencing targeting 275 genes revealed pathogenically relevant mutations of <i>CD79B</i>, <i>MyD88</i>, <i>TP53</i>, <i>TBL1XR1</i>, and <i>PIM1</i> genes, indicating that this lymphoma would be best classified as MCD/C5 DLBCL, an ABC subtype. Despite an initial good clinical response to BTK inhibitor ibrutinib, anti-CD20 antibody rituxan, alkylating agent bendamustine, and hematopoietic stem-cell transplant, the lymphoma relapsed, accompanied by morphologic and molecular evidence of disease progression. Specifically, the recurrent tumor developed loss of <i>TP53</i> heterozygosity (LOH) and additional chromosomal changes central to ABC DLBCL pathogenesis, such as <i>PRDM1</i> loss. Acquired resistance to ibrutinib and rituxan was indicated by the emergence of <i>BTK</i> and <i>FOXO1</i> mutations, respectively, as well as apparent activation of alternative cell-activation pathways, through copy-number alterations (CNAs), detected by high-resolution chromosomal microarrays. In vitro, studies of relapsed lymphoma cells confirmed resistance to standard BTK inhibitors but sensitivity to vecabrutinib, a noncovalent inhibitor active against both wild-type as well as mutated BTK. In summary, we provide in-depth molecular characterization of a de novo leukemic DLBCL and discuss mechanisms that may have contributed to the lymphoma establishment, progression, and development of drug resistance.</p>","PeriodicalId":10360,"journal":{"name":"Cold Spring Harbor Molecular Case Studies","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2024-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10815299/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41093560","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}