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1.
Cell ; 175(7): 1972-1988.e16, 2018 12 13.
Article in English | MEDLINE | ID: mdl-30550791

ABSTRACT

In vitro cancer cultures, including three-dimensional organoids, typically contain exclusively neoplastic epithelium but require artificial reconstitution to recapitulate the tumor microenvironment (TME). The co-culture of primary tumor epithelia with endogenous, syngeneic tumor-infiltrating lymphocytes (TILs) as a cohesive unit has been particularly elusive. Here, an air-liquid interface (ALI) method propagated patient-derived organoids (PDOs) from >100 human biopsies or mouse tumors in syngeneic immunocompetent hosts as tumor epithelia with native embedded immune cells (T, B, NK, macrophages). Robust droplet-based, single-cell simultaneous determination of gene expression and immune repertoire indicated that PDO TILs accurately preserved the original tumor T cell receptor (TCR) spectrum. Crucially, human and murine PDOs successfully modeled immune checkpoint blockade (ICB) with anti-PD-1- and/or anti-PD-L1 expanding and activating tumor antigen-specific TILs and eliciting tumor cytotoxicity. Organoid-based propagation of primary tumor epithelium en bloc with endogenous immune stroma should enable immuno-oncology investigations within the TME and facilitate personalized immunotherapy testing.


Subject(s)
Models, Immunological , Neoplasms, Experimental/immunology , Organoids/immunology , Receptors, Antigen, T-Cell/immunology , Tumor Microenvironment/immunology , Animals , B7-H1 Antigen/immunology , Coculture Techniques , Female , Humans , Immunotherapy , Male , Mice , Mice, Inbred BALB C , Neoplasm Proteins/immunology , Neoplasms, Experimental/pathology , Neoplasms, Experimental/therapy , Organoids/pathology
2.
Cell ; 173(2): 291-304.e6, 2018 04 05.
Article in English | MEDLINE | ID: mdl-29625048

ABSTRACT

We conducted comprehensive integrative molecular analyses of the complete set of tumors in The Cancer Genome Atlas (TCGA), consisting of approximately 10,000 specimens and representing 33 types of cancer. We performed molecular clustering using data on chromosome-arm-level aneuploidy, DNA hypermethylation, mRNA, and miRNA expression levels and reverse-phase protein arrays, of which all, except for aneuploidy, revealed clustering primarily organized by histology, tissue type, or anatomic origin. The influence of cell type was evident in DNA-methylation-based clustering, even after excluding sites with known preexisting tissue-type-specific methylation. Integrative clustering further emphasized the dominant role of cell-of-origin patterns. Molecular similarities among histologically or anatomically related cancer types provide a basis for focused pan-cancer analyses, such as pan-gastrointestinal, pan-gynecological, pan-kidney, and pan-squamous cancers, and those related by stemness features, which in turn may inform strategies for future therapeutic development.


Subject(s)
Neoplasms/pathology , Aneuploidy , Chromosomes/genetics , Cluster Analysis , CpG Islands , DNA Methylation , Databases, Factual , Humans , MicroRNAs/metabolism , Mutation , Neoplasm Proteins/genetics , Neoplasm Proteins/metabolism , Neoplasms/genetics , RNA, Messenger/metabolism
3.
Cell ; 173(2): 321-337.e10, 2018 04 05.
Article in English | MEDLINE | ID: mdl-29625050

ABSTRACT

Genetic alterations in signaling pathways that control cell-cycle progression, apoptosis, and cell growth are common hallmarks of cancer, but the extent, mechanisms, and co-occurrence of alterations in these pathways differ between individual tumors and tumor types. Using mutations, copy-number changes, mRNA expression, gene fusions and DNA methylation in 9,125 tumors profiled by The Cancer Genome Atlas (TCGA), we analyzed the mechanisms and patterns of somatic alterations in ten canonical pathways: cell cycle, Hippo, Myc, Notch, Nrf2, PI-3-Kinase/Akt, RTK-RAS, TGFß signaling, p53 and ß-catenin/Wnt. We charted the detailed landscape of pathway alterations in 33 cancer types, stratified into 64 subtypes, and identified patterns of co-occurrence and mutual exclusivity. Eighty-nine percent of tumors had at least one driver alteration in these pathways, and 57% percent of tumors had at least one alteration potentially targetable by currently available drugs. Thirty percent of tumors had multiple targetable alterations, indicating opportunities for combination therapy.


Subject(s)
Databases, Genetic , Neoplasms/pathology , Signal Transduction/genetics , Genes, Neoplasm , Humans , Neoplasms/genetics , Phosphatidylinositol 3-Kinases/genetics , Phosphatidylinositol 3-Kinases/metabolism , Transforming Growth Factor beta/genetics , Transforming Growth Factor beta/metabolism , Tumor Suppressor Protein p53/genetics , Tumor Suppressor Protein p53/metabolism , Wnt Proteins/genetics , Wnt Proteins/metabolism
4.
Cell ; 171(3): 540-556.e25, 2017 Oct 19.
Article in English | MEDLINE | ID: mdl-28988769

ABSTRACT

We report a comprehensive analysis of 412 muscle-invasive bladder cancers characterized by multiple TCGA analytical platforms. Fifty-eight genes were significantly mutated, and the overall mutational load was associated with APOBEC-signature mutagenesis. Clustering by mutation signature identified a high-mutation subset with 75% 5-year survival. mRNA expression clustering refined prior clustering analyses and identified a poor-survival "neuronal" subtype in which the majority of tumors lacked small cell or neuroendocrine histology. Clustering by mRNA, long non-coding RNA (lncRNA), and miRNA expression converged to identify subsets with differential epithelial-mesenchymal transition status, carcinoma in situ scores, histologic features, and survival. Our analyses identified 5 expression subtypes that may stratify response to different treatments.


Subject(s)
Urinary Bladder Neoplasms/genetics , Urinary Bladder Neoplasms/pathology , Aged , Cluster Analysis , DNA Methylation , Humans , MicroRNAs/genetics , Middle Aged , Muscle, Smooth/pathology , RNA, Long Noncoding/genetics , Survival Analysis , Urinary Bladder/pathology , Urinary Bladder Neoplasms/epidemiology , Urinary Bladder Neoplasms/therapy
5.
Mol Cell ; 83(13): 2347-2356.e8, 2023 Jul 06.
Article in English | MEDLINE | ID: mdl-37311462

ABSTRACT

Oncogenic mutations in isocitrate dehydrogenases 1 and 2 (IDH1/2) produce 2-hydroxyglutarate (2HG), which inhibits dioxygenases that modulate chromatin dynamics. The effects of 2HG have been reported to sensitize IDH tumors to poly-(ADP-ribose) polymerase (PARP) inhibitors. However, unlike PARP-inhibitor-sensitive BRCA1/2 tumors, which exhibit impaired homologous recombination, IDH-mutant tumors have a silent mutational profile and lack signatures associated with impaired homologous recombination. Instead, 2HG-producing IDH mutations lead to a heterochromatin-dependent slowing of DNA replication accompanied by increased replication stress and DNA double-strand breaks. This replicative stress manifests as replication fork slowing, but the breaks are repaired without a significant increase in mutation burden. Faithful resolution of replicative stress in IDH-mutant cells is dependent on poly-(ADP-ribosylation). Treatment with PARP inhibitors increases DNA replication but results in incomplete DNA repair. These findings demonstrate a role for PARP in the replication of heterochromatin and further validate PARP as a therapeutic target in IDH-mutant tumors.


Subject(s)
BRCA1 Protein , Neoplasms , Humans , BRCA1 Protein/genetics , Heterochromatin/genetics , Poly(ADP-ribose) Polymerase Inhibitors/pharmacology , BRCA2 Protein/genetics , Homologous Recombination/genetics , Neoplasms/drug therapy , Neoplasms/genetics , Mutation , Isocitrate Dehydrogenase/genetics
6.
Nature ; 622(7981): 41-47, 2023 Oct.
Article in English | MEDLINE | ID: mdl-37794265

ABSTRACT

Scientists have been trying to identify every gene in the human genome since the initial draft was published in 2001. In the years since, much progress has been made in identifying protein-coding genes, currently estimated to number fewer than 20,000, with an ever-expanding number of distinct protein-coding isoforms. Here we review the status of the human gene catalogue and the efforts to complete it in recent years. Beside the ongoing annotation of protein-coding genes, their isoforms and pseudogenes, the invention of high-throughput RNA sequencing and other technological breakthroughs have led to a rapid growth in the number of reported non-coding RNA genes. For most of these non-coding RNAs, the functional relevance is currently unclear; we look at recent advances that offer paths forward to identifying their functions and towards eventually completing the human gene catalogue. Finally, we examine the need for a universal annotation standard that includes all medically significant genes and maintains their relationships with different reference genomes for the use of the human gene catalogue in clinical settings.


Subject(s)
Genes , Genome, Human , Molecular Sequence Annotation , Protein Isoforms , Humans , Genome, Human/genetics , Molecular Sequence Annotation/standards , Molecular Sequence Annotation/trends , Protein Isoforms/genetics , Human Genome Project , Pseudogenes , RNA/genetics
8.
Blood ; 2024 Sep 10.
Article in English | MEDLINE | ID: mdl-39255410

ABSTRACT

Recent introduction of two different lymphoma classifications has raised concerns about consistency in diagnosis, management, and clinical trial enrollment. Data from a large cohort reflecting real-world clinical practice suggest that differences between the classifications will impact <1% of non-Hodgkin lymphomas.

9.
Mol Psychiatry ; 2024 May 23.
Article in English | MEDLINE | ID: mdl-38783055

ABSTRACT

Pharmacogenomic testing has emerged as an aid in clinical decision making for psychiatric providers, but more data is needed regarding its utility in clinical practice and potential impact on patient care. In this cross-sectional study, we determined the real-world prevalence of pharmacogenomic actionability in patients receiving psychiatric care. Potential actionability was based on the prevalence of CYP2C19 and CYP2D6 phenotypes, including CYP2D6 allele-specific copy number variations (CNVs). Combined actionability additionally incorporated CYP2D6 phenoconversion and the novel CYP2C-TG haplotype in patients with available medication data. Across 15,000 patients receiving clinical pharmacogenomic testing, 65% had potentially actionable CYP2D6 and CYP2C19 phenotypes, and phenotype assignment was impacted by CYP2D6 allele-specific CNVs in 2% of all patients. Of 4114 patients with medication data, 42% had CYP2D6 phenoconversion from drug interactions and 20% carried a novel CYP2C haplotype potentially altering actionability. A total of 87% had some form of potential actionability from genetic findings and/or phenoconversion. Genetic variation detected via next-generation sequencing led to phenotype reassignment in 22% of individuals overall (2% in CYP2D6 and 20% in CYP2C19). Ultimately, pharmacogenomic testing using next-generation sequencing identified potential actionability in most patients receiving psychiatric care. Early pharmacogenomic testing may provide actionable insights to aid clinicians in drug prescribing to optimize psychiatric care.

10.
Article in English | MEDLINE | ID: mdl-39182630

ABSTRACT

BACKGROUND: Deficiency of adenosine deaminase (ADA or ADA1) has broad clinical and genetic heterogeneity. Screening techniques can identify asymptomatic infants whose phenotype and prognosis are indeterminate, and who may carry ADA variants of unknown significance. OBJECTIVE: We systematically assessed the pathogenic potential of rare ADA missense variants to better define the relationship of genotype to red blood cell (RBC) total deoxyadenosine nucleotide (dAXP) content and to phenotype. METHODS: We expressed 46 ADA missense variants in the ADA-deficient SØ3834 strain of Escherichia coli and defined genotype categories (GCs) ranked I to IV by increasing expressed ADA activity. We assessed relationships among GC rank, RBC dAXP, and phenotype in 58 reference patients with 50 different genotypes. We used our GC ranking system to benchmark AlphaMissense for predicting variant pathogenicity, and we used a minigene assay to identify exonic splicing variants in ADA exon 9. RESULTS: The 46 missense variants expressed ∼0.001% to ∼70% of wild-type ADA activity (40% had <0.05% of wild-type ADA activity and 50% expressed >1%). RBC dAXP ranged from undetectable to >75% of total adenine nucleotides and correlated well with phenotype. Both RBC dAXP and clinical severity were inversely related to total ADA activity expressed by both inherited variants. Our GC scoring system performed better than AlphaMissense in assessing variant pathogenicity, particularly for less deleterious variants. CONCLUSION: For ADA deficiency, pathogenicity is a continuum and conditional, depending on the total ADA activity contributed by both inherited variants as indicated by GC rank. However, in patients with indeterminate phenotype identified by screening, RBC dAXP measured at diagnosis may have greater prognostic value than GC rank.

11.
Lab Invest ; 104(11): 102147, 2024 Oct 09.
Article in English | MEDLINE | ID: mdl-39389311

ABSTRACT

Angioimmunoblastic T-cell lymphoma (AITL), the most common form of peripheral T-cell lymphoma, originates from follicular helper T (Tfh) cells and is notably resistant to current treatments. The disease progression and maintenance, at least in early stages, are driven by a complex interplay between neoplastic Tfh and clusters of B-cells within the tumor microenvironment, mirroring the functional crosstalk observed inside germinal centers. This interaction is further complicated by recurrent mutations, such as TET2 and DNMT3A, which are present in both Tfh cells and B-cells. These findings suggest that the symbiotic relationship between these 2 cell types could represent a therapeutic vulnerability. This review examines the key components and signaling mechanisms involved in the synapses between B-cells and Tfh cells, emphasizing their significant role in the pathobiology of AITL and potential as therapeutic targets.

12.
Am J Hematol ; 99(11): 2096-2107, 2024 Nov.
Article in English | MEDLINE | ID: mdl-39152767

ABSTRACT

In classical Hodgkin lymphoma (cHL), responsiveness to immune-checkpoint blockade (ICB) is associated with specific tumor microenvironment (TME) and peripheral blood features. The role of ICB in nodular lymphocyte predominant Hodgkin lymphoma (NLPHL) is not established. To gain insights into its potential in NLPHL, we compared TME and peripheral blood signatures between HLs using an integrative multiomic analysis. A discovery/validation approach in 121 NLPHL and 114 cHL patients highlighted >2-fold enrichment in programmed cell death-1 (PD-1) and T-cell Ig and ITIM domain (TIGIT) gene expression for NLPHL versus cHL. Multiplex imaging showed marked increase in intra-tumoral protein expression of PD-1+ (and/or TIGIT+) CD4+ T-cells and PD-1+CD8+ T-cells in NLPHL compared to cHL. This included T-cells that rosetted with lymphocyte predominant (LP) and Hodgkin Reed-Sternberg (HRS) cells. In NLPHL, intra-tumoral PD-1+CD4+ T-cells frequently expressed TCF-1, a marker of heightened T-cell response to ICB. The peripheral blood signatures between HLs were also distinct, with higher levels of PD-1+TIGIT+ in TH1, TH2, and regulatory CD4+ T-cells in NLPHL versus cHL. Circulating PD-1+CD4+ had high levels of TCF-1. Notably, in both lymphomas, highly expanded populations of clonal TIGIT+PD-1+CD4+ and TIGIT+PD-1+CD8+ T-cells in the blood were also present in the TME, indicating that immune-checkpoint expressing T-cells circulated between intra-tumoral and blood compartments. In in vitro assays, ICB was capable of reducing rosette formation around LP and HRS cells, suggesting that disruption of rosetting may be a mechanism of action of ICB in HL. Overall, results indicate that further evaluation of ICB is warranted in NLPHL.


Subject(s)
Biomarkers, Tumor , Hodgkin Disease , Programmed Cell Death 1 Receptor , Receptors, Immunologic , Tumor Microenvironment , Humans , Hodgkin Disease/blood , Hodgkin Disease/immunology , Hodgkin Disease/diagnosis , Receptors, Immunologic/blood , Male , Female , Adult , Biomarkers, Tumor/blood , Middle Aged , CD4-Positive T-Lymphocytes/immunology , CD8-Positive T-Lymphocytes/immunology , Aged
13.
Am J Hematol ; 99(3): 408-421, 2024 03.
Article in English | MEDLINE | ID: mdl-38217361

ABSTRACT

To address the current and long-term unmet health needs of the growing population of non-Hodgkin lymphoma (NHL) patients, we established the Lymphoma Epidemiology of Outcomes (LEO) cohort study (NCT02736357; https://leocohort.org/). A total of 7735 newly diagnosed patients aged 18 years and older with NHL were prospectively enrolled from 7/1/2015 to 5/31/2020 at 8 academic centers in the United States. The median age at diagnosis was 62 years (range, 18-99). Participants came from 49 US states and included 538 Black/African-Americans (AA), 822 Hispanics (regardless of race), 3386 women, 716 age <40 years, and 1513 rural residents. At study baseline, we abstracted clinical, pathology, and treatment data; banked serum/plasma (N = 5883, 76.0%) and germline DNA (N = 5465, 70.7%); constructed tissue microarrays for four major NHL subtypes (N = 1189); and collected quality of life (N = 5281, 68.3%) and epidemiologic risk factor (N = 4489, 58.0%) data. Through August 2022, there were 1492 deaths. Compared to population-based SEER data (2015-2019), LEO participants had a similar distribution of gender, AA race, Hispanic ethnicity, and NHL subtype, while LEO was underrepresented for patients who were Asian and aged 80 years and above. Observed overall survival rates for LEO at 1 and 2 years were similar to population-based SEER rates for indolent B-cell (follicular and marginal zone) and T-cell lymphomas, but were 10%-15% higher than SEER rates for aggressive B-cell subtypes (diffuse large B-cell and mantle cell). The LEO cohort is a robust and comprehensive national resource to address the role of clinical, tumor, host genetic, epidemiologic, and other biologic factors in NHL prognosis and survivorship.


Subject(s)
Lymphoma, Non-Hodgkin , Quality of Life , Humans , Female , United States/epidemiology , Adolescent , Young Adult , Adult , Middle Aged , Aged , Aged, 80 and over , Cohort Studies , Lymphoma, Non-Hodgkin/diagnosis , B-Lymphocytes/pathology , Prognosis
14.
Epidemiol Infect ; 152: e12, 2024 Jan 08.
Article in English | MEDLINE | ID: mdl-38185825

ABSTRACT

Salmonella enterica continues to be a leading cause of foodborne morbidity worldwide. A quantitative risk assessment model was developed to evaluate the impact of pathogen enumeration and serotyping strategies on public health after consumption of undercooked contaminated ground turkey in the USA. The risk assessment model predicted more than 20,000 human illnesses annually that would result in ~700 annual reported cases. Removing ground turkey lots contaminated with Salmonella exceeding 10 MPN/g, 1 MPN/g, and 1 MPN/25 g would decrease the mean number of illnesses by 38.2, 73.1, and 95.0%, respectively. A three-class mixed sampling plan was tested to allow the detection of positive lots above threshold levels with 2-6 (c = 1) and 3-8 samples per lot (c = 2) using 25-g and 325-g sample sizes for a 95% probability of rejecting a contaminated lot. Removal of positive lots with the presence of highly virulent serotypes would decrease the number of illnesses by 44.2-87.0%. Based on these model prediction results, risk management strategies should incorporate pathogen enumeration and/or serotyping. This would have a direct impact on illness incidence linking public health outcomes with measurable food safety objectives, at the cost of diverting production lots.


Subject(s)
Salmonella enterica , Salmonella , Animals , Humans , Serotyping , Turkeys , Risk Management , Outcome Assessment, Health Care
15.
Med Educ ; 58(8): 952-960, 2024 08.
Article in English | MEDLINE | ID: mdl-38273430

ABSTRACT

INTRODUCTION: Medical residents may be required to handle health care management (HCM) tasks alongside their clinical duties, despite not having received training to perform them. However, little research has been done on how medical residents acquire HCM skills at the workplace and how these experiences impact their learning. METHODS: We completed a qualitative research study using the Constructivist Grounded Theory approach inform by the Figured World theory. To gather data, we held focus groups and conducted semi-structured interviews with 22 medical residents from various disciplines and learning levels at Pontificia Universidad Javeriana. We utilised iterative data collection and analysis, constant comparison methods and theoretical sampling to construct our findings. RESULTS: We constructed two different worlds to represent how residents acquire HCM skills: the non-managing physician and the physician-as-manager. The former was characterised by a discourse that underplayed the role of the HCM tasks as part of residents' training, was full of negative interactions with the health care team and limited residents' agency. In the latter, residents collaborated and learned from health care team members, had supervisors who modelled how to incorporate HCM tasks into daily activities and expanded residents' agency. Residents developed their professional identity according to the world they were introduced into. DISCUSSION: Educational leaders must understand that the non-managing physician figured world gives residents a feeling of uprooting and discomfort when carrying out this type of tasks. To transform this world into the physician-as-manager, it is necessary to reconfigure some workplace hierarchies, consolidate interprofessional collaborations and change the discourse perpetuated by influential role models. Supervisors must also strengthen their knowledge of HCM and improve its integration into clinical practice. Any effort to train residents on HCM competencies could be lost if the workplace underscores their value in patient care.


Subject(s)
Grounded Theory , Internship and Residency , Qualitative Research , Workplace , Humans , Focus Groups , Female , Male , Clinical Competence , Adult
16.
Med Educ ; 2024 Aug 06.
Article in English | MEDLINE | ID: mdl-39104362

ABSTRACT

The pivotal importance of workplace learning (WPL) within health professions education has elevated its understanding and improvement to a major research priority. From a sociocultural learning theory perspective, WPL is inherently situated and context-specific. This means that the health care settings in which (future) health care professionals are trained will impact how and what is learned. However, to what extent is the research performed thus far transferable across professional contexts, cultures and borders? To what extent has WPL research sufficiently addressed the contextual characteristics of WPL to enable the evaluation of its transferability? To what extent have methodological and theoretical approaches enabled the building of understanding across contexts? We propose that heightening the transferability of WPL research as well as opening up the conversation to more diverse WPL contexts, settings and cultures will require mapping context and theoretical engagement. To explore what theoretical engagement may afford to our understanding of the influence of context on WPL, we use two theories: Landscapes of Practice and Figured Worlds. These theories with sociocultural groundings provide concrete lenses to understand the interplay between the individual and the context. We conclude with implications for research and practice and advocate for more attention to research practices that may deepen our understanding and heighten the transferability of workplace learning research.

17.
Med Educ ; 2024 Oct 20.
Article in English | MEDLINE | ID: mdl-39428833

ABSTRACT

INTRODUCTION: Attrition in surgical residencies remains a significant issue, with traditional research focusing mainly on individual and programme factors. This study explores the role of clinical teachers (CTs) in influencing attrition rates. CTs are essential in moulding residents' training, serving both as enablers of workplace learning and guardians of their medical fields. METHODS: We employed a hermeneutic phenomenology framework to understand the sociocultural impacts on attrition. Data were collected through semi-structured interviews involving 19 CTs, 3 residents who left the programme and 2 who underwent remediation, following a six-step hermeneutic phenomenological analysis process. RESULTS: The entrenched 'good surgeon' narrative within the department demanded selflessness and total dedication, which CTs reinforced, thereby normalising a rigorous and challenging environment. This has led to attrition when residents fail to meet these challenges or choose to disengage from the system. We illustrated that CTs were pivotal in perpetuating these expectations, contributing significantly to resident attrition. CONCLUSIONS: CTs played a crucial role in resident attrition by enforcing a stringent cultural norm within surgical training programmes. Addressing this issue requires a visible change in CTs' role to foster a more supportive educational environment. Emphasising the beneficial aspects of the 'good surgeon' narrative and mitigating its adverse impacts is essential for reducing attrition rates and assisting all residents, including those facing challenges, in successfully completing their training.

18.
Breast Cancer Res ; 25(1): 58, 2023 05 25.
Article in English | MEDLINE | ID: mdl-37231433

ABSTRACT

BACKGROUND: Endocrine-resistant HR+/HER2- breast cancer (BC) and triple-negative BC (TNBC) are of interest for molecularly informed treatment due to their aggressive natures and limited treatment profiles. Patients of African Ancestry (AA) experience higher rates of TNBC and mortality than European Ancestry (EA) patients, despite lower overall BC incidence. Here, we compare the molecular landscapes of AA and EA patients with HR+/HER2- BC and TNBC in a real-world cohort to promote equity in precision oncology by illuminating the heterogeneity of potentially druggable genomic and transcriptomic pathways. METHODS: De-identified records from patients with TNBC or HR+/HER2- BC in the Tempus Database were randomly selected (N = 5000), with most having stage IV disease. Mutations, gene expression, and transcriptional signatures were evaluated from next-generation sequencing data. Genetic ancestry was estimated from DNA-seq. Differences in mutational prevalence, gene expression, and transcriptional signatures between AA and EA were compared. EA patients were used as the reference population for log fold-changes (logFC) in expression. RESULTS: After applying inclusion criteria, 3433 samples were evaluated (n = 623 AA and n = 2810 EA). Observed patterns of dysregulated pathways demonstrated significant heterogeneity among the two groups. Notably, PIK3CA mutations were significantly lower in AA HR+/HER2- tumors (AA = 34% vs. EA = 42%, P < 0.05) and the overall cohort (AA = 28% vs. EA = 37%, P = 2.08e-05). Conversely, KMT2C mutation was significantly more frequent in AA than EA TNBC (23% vs. 12%, P < 0.05) and HR+/HER2- (24% vs. 15%, P = 3e-03) tumors. Across all subtypes and stages, over 8000 genes were differentially expressed between the two ancestral groups including RPL10 (logFC = 2.26, P = 1.70e-162), HSPA1A (logFC = - 2.73, P = 2.43e-49), ATRX (logFC = - 1.93, P = 5.89e-83), and NUTM2F (logFC = 2.28, P = 3.22e-196). Ten differentially expressed gene sets were identified among stage IV HR+/HER2- tumors, of which four were considered relevant to BC treatment and were significantly enriched in EA: ERBB2_UP.V1_UP (P = 3.95e-06), LTE2_UP.V1_UP (P = 2.90e-05), HALLMARK_FATTY_ACID_METABOLISM (P = 0.0073), and HALLMARK_ANDROGEN_RESPONSE (P = 0.0074). CONCLUSIONS: We observed significant differences in mutational spectra, gene expression, and relevant transcriptional signatures between patients with genetically determined African and European ancestries, particularly within the HR+/HER2- BC and TNBC subtypes. These findings could guide future development of treatment strategies by providing opportunities for biomarker-informed research and, ultimately, clinical decisions for precision oncology care in diverse populations.


Subject(s)
Breast Neoplasms , Triple Negative Breast Neoplasms , Female , Humans , Black People/genetics , Breast Neoplasms/ethnology , Breast Neoplasms/pathology , Mutation , Precision Medicine , Triple Negative Breast Neoplasms/ethnology , Triple Negative Breast Neoplasms/pathology , White People
19.
Blood ; 137(15): 2103-2113, 2021 04 15.
Article in English | MEDLINE | ID: mdl-33270827

ABSTRACT

Venous thromboembolism (VTE) associated with cancer (CAT) is a well-described complication of cancer and a leading cause of death in patients with cancer. The purpose of this study was to assess potential associations of molecular signatures with CAT, including tumor-specific mutations and the presence of clonal hematopoiesis. We analyzed deep-coverage targeted DNA-sequencing data of >14 000 solid tumor samples using the Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets platform to identify somatic alterations associated with VTE. End point was defined as the first instance of cancer-associated pulmonary embolism and/or proximal/distal lower extremity deep vein thrombosis. Cause-specific Cox proportional hazards regression was used, adjusting for pertinent clinical covariates. Of 11 695 evaluable individuals, 72% had metastatic disease at time of analysis. Tumor-specific mutations in KRAS (hazard ratio [HR], 1.34; 95% confidence interval (CI), 1.09-1.64; adjusted P = .08), STK11 (HR, 2.12; 95% CI, 1.55-2.89; adjusted P < .001), KEAP1 (HR, 1.84; 95% CI, 1.21-2.79; adjusted P = .07), CTNNB1 (HR, 1.73; 95% CI, 1.15-2.60; adjusted P = .09), CDKN2B (HR, 1.45; 95% CI, 1.13-1.85; adjusted P = .07), and MET (HR, 1.83; 95% CI, 1.15-2.92; adjusted P = .09) were associated with a significantly increased risk of CAT independent of tumor type. Mutations in SETD2 were associated with a decreased risk of CAT (HR, 0.35; 95% CI, 0.16-0.79; adjusted P = .09). The presence of clonal hematopoiesis was not associated with an increased VTE rate. This is the first large-scale analysis to elucidate tumor-specific genomic events associated with CAT. Somatic tumor mutations of STK11, KRAS, CTNNB1, KEAP1, CDKN2B, and MET were associated with an increased risk of VTE in patients with solid tumors. Further analysis is needed to validate these findings and identify additional molecular signatures unique to individual tumor types.


Subject(s)
Neoplasms/complications , Venous Thromboembolism/etiology , Aged , Genetic Predisposition to Disease , Genomics , Humans , Middle Aged , Mutation , Neoplasms/genetics , Risk Factors , Venous Thromboembolism/genetics
20.
Histopathology ; 83(1): 143-148, 2023 Jul.
Article in English | MEDLINE | ID: mdl-36994939

ABSTRACT

Chimeric antigen receptor (CAR) T-cells anti-CD30 is an innovative therapeutic option that has been used to treat cases of refractory/relapsed (R/R) classic Hodgkin lymphoma (CHL). Limited data are available regarding the CD30 expression status of patients who relapsed after this therapy. This is the first study to show decreased CD30 expression in R/R CHL in patients (n = 5) who underwent CAR T-cell therapy in our institution between 2018 and 2022. Although conventional immunohistochemical assays showed decreased CD30 expression in neoplastic cells in all cases (8/8) the tyramide amplification assay and RNAScope in situ hybridisation detected CD30 expression at different levels in 100% (n = 8/8) and 75% (n = 3/4), respectively. Hence, our findings document that certain levels of CD30 expression are retained by the neoplastic cells. This is not only of biological interest but also diagnostically important, as detection of CD30 is an essential factor in establishing a diagnosis of CHL.


Subject(s)
Hodgkin Disease , Immunoconjugates , Humans , Hodgkin Disease/pathology , Ki-1 Antigen/metabolism , Immunotherapy, Adoptive , Immunoconjugates/therapeutic use
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