Centre for Cancer Research - Research Publications
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ItemNo Preview AvailableSingle-cell multiomics reveal the scale of multilayered adaptations enabling CLL relapse during venetoclax therapy(AMER SOC HEMATOLOGY, 2022-11-17)Venetoclax (VEN) inhibits the prosurvival protein BCL2 to induce apoptosis and is a standard therapy for chronic lymphocytic leukemia (CLL), delivering high complete remission rates and prolonged progression-free survival in relapsed CLL but with eventual loss of efficacy. A spectrum of subclonal genetic changes associated with VEN resistance has now been described. To fully understand clinical resistance to VEN, we combined single-cell short- and long-read RNA-sequencing to reveal the previously unappreciated scale of genetic and epigenetic changes underpinning acquired VEN resistance. These appear to be multilayered. One layer comprises changes in the BCL2 family of apoptosis regulators, especially the prosurvival family members. This includes previously described mutations in BCL2 and amplification of the MCL1 gene but is heterogeneous across and within individual patient leukemias. Changes in the proapoptotic genes are notably uncommon, except for single cases with subclonal losses of BAX or NOXA. Much more prominent was universal MCL1 gene upregulation. This was driven by an overlying layer of emergent NF-κB (nuclear factor kappa B) activation, which persisted in circulating cells during VEN therapy. We discovered that MCL1 could be a direct transcriptional target of NF-κB. Both the switch to alternative prosurvival factors and NF-κB activation largely dissipate following VEN discontinuation. Our studies reveal the extent of plasticity of CLL cells in their ability to evade VEN-induced apoptosis. Importantly, these findings pinpoint new approaches to circumvent VEN resistance and provide a specific biological justification for the strategy of VEN discontinuation once a maximal response is achieved rather than maintaining long-term selective pressure with the drug.
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ItemEnrichment of BTK Leu528Trp mutations in patients with CLL on zanubrutinib: potential for pirtobrutinib cross-resistance(ELSEVIER, 2022-10-25)The covalent Bruton's tyrosine kinase inhibitors (BTKis) are highly effective for the treatment of chronic lymphocytic leukemia (CLL). The dominant resistance mechanism observed with the BTKi ibrutinib is the development of BTK Cys481 codon mutations. Whether a similar resistance mutation profile exists for the newer-generation, more selective BTKi zanubrutinib is unknown. In samples referred for diagnostic next-generation sequencing in patients with progressive CLL, we observed an enrichment in the kinase-dead BTK Leu528Trp mutation in patients treated with zanubrutinib compared with ibrutinib (54%; 7 of 13 vs 4%; 1 of 24, P = .001). We describe 2 patients with BTK Leu528Trp mutations who showed clinical cross-resistance and progressive enrichment of the BTK Leu528Trp mutation over time when treated with the noncovalent BTKi pirtobrutinib. Both patients subsequently responded to venetoclax-based treatment. In summary, we have identified an enrichment of the BTK Leu528Trp mutation arising in patients treated with zanubrutinib that may impart cross-resistance to the noncovalent inhibitor pirtobrutinib and therefore may have implications for sequencing of these treatments in CLL.
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ItemNo Preview AvailableTrajectories of glycemic control with clinical pharmacy specialist management of veterans with type 2 diabetes.(Elsevier BV, 2022-06)BACKGROUND: Improved control of glycemic control likely lowers the risk of diabetes complications and clinical pharmacy specialist (CPS) services can improve glycemic control. Though the pattern of control may also matter in terms of outcomes. OBJECTIVES: The objective of this study was to examine the longitudinal trajectories of HbA1c among a large population of Veterans with type 2 diabetes who received CPS-led diabetes management. METHODS: This is an observational, multicenter cohort study of Veterans with type-2 diabetes managed by CPSs between 7/1/2013 and 7/1/2017 with baseline glycosylated hemoglobin (HbA1c) level ≥8%. Two years of HbA1c measurements were used to group patients into distinct patterns of HbA1c trajectories over time using group-based trajectory modeling. Characteristics associated with successful HbA1c trajectories and association of assigned trajectories with all-cause and diabetes-related hospitalizations were analyzed using logistic regression. RESULTS: A total of 4119 Veterans were included and able to be successfully segmented into six distinct HbA1c trajectory groups over time: High Gradually Decreasing (n = 325, 7.9%), Moderate Early Decline (n = 1692, 41.1%), Large Early Decline (n = 231, 5.6%), Uncontrolled Stable (n = 1468, 35.6%), Early Decline/Subsequent Increase (n = 266, 6.5%), and Very Uncontrolled Stable (n = 137, 3.3%). The distinguishing factor between successful and less successful trajectories appears to be the progress made within the first six months of pharmacist management. CONCLUSIONS: Significant variability exists in the pattern of glycemic control over time of type 2 diabetes patients managed by clinical pharmacy specialists. Limited resources should be first prioritized to managing patients with very elevated HbA1c and into the first six months of CPS management.
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ItemGermline MBD4 deficiency causes a multi-tumor predisposition syndrome(CELL PRESS, 2022-05-05)We report an autosomal recessive, multi-organ tumor predisposition syndrome, caused by bi-allelic loss-of-function germline variants in the base excision repair (BER) gene MBD4. We identified five individuals with bi-allelic MBD4 variants within four families and these individuals had a personal and/or family history of adenomatous colorectal polyposis, acute myeloid leukemia, and uveal melanoma. MBD4 encodes a glycosylase involved in repair of G:T mismatches resulting from deamination of 5'-methylcytosine. The colorectal adenomas from MBD4-deficient individuals showed a mutator phenotype attributable to mutational signature SBS1, consistent with the function of MBD4. MBD4-deficient polyps harbored somatic mutations in similar driver genes to sporadic colorectal tumors, although AMER1 mutations were more common and KRAS mutations less frequent. Our findings expand the role of BER deficiencies in tumor predisposition. Inclusion of MBD4 in genetic testing for polyposis and multi-tumor phenotypes is warranted to improve disease management.
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ItemLong-term Follow-up of Patients with Relapsed or Refractory Non-Hodgkin Lymphoma Treated with Venetoclax in a Phase I, First-in-Human Study(AMER ASSOC CANCER RESEARCH, 2021-09-01)PURPOSE: We previously reported a 44% overall response rate (ORR) with the oral BCL-2 inhibitor venetoclax in a phase I study of relapsed/refractory non-Hodgkin lymphoma (NHL). Complete response (CR) was observed in patients with mantle cell lymphoma [(MCL), 21%, n = 6/28] and follicular lymphoma [(FL), 17%, n = 5/29], and partial response (PR) noted in several patients with Waldenström macroglobulinemia (WM), and marginal zone lymphoma (MZL). Here, we report the long-term outcomes of these four cohorts. PATIENTS AND METHODS: All patients (n = 106) received venetoclax monotherapy in dose cohorts of 200 to 1,200 mg daily until disease progression or unacceptable toxicity. ORR, progression-free survival (PFS), duration of response (DoR), and adverse events (AEs) were evaluated. RESULTS: At a median follow-up of 38.5 months (range, 30.0-46.5), the median PFS for all 106 patients was 5.4 [95% confidence interval (CI), 3.5-8.4] months (FL, 10.8; MCL, 11.3; MZL, 21.2; and WM, 30.4). The median DoR was 14.9 (95% CI, 9.7-27.6) months (FL, 26.6; MCL, 15.7; MZL, 20.1; and WM, 25.3). Achievement of CR versus PR predicted longer DoR in both MCL (31.5 vs. 10.1 months) and FL (37.6 vs. 9.7 months). All grade hematologic AEs were infrequent: neutropenia (19%), anemia (19%), and thrombocytopenia (17%), with no new cytopenias after 2 years on therapy. Nonhematologic AEs included nausea (49%), diarrhea (46%), fatigue (44%), with decreased incidence after 1 year. CONCLUSIONS: Venetoclax monotherapy has a manageable safety profile and achieves durable responses in a subset of patients with FL, MCL, WM, and MZL, particularly in those who achieve CR. Further research is warranted on combination strategies to enhance the durability of response to venetoclax.
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ItemSingle-cell sequencing demonstrates complex resistance landscape in CLL and MCL treated with BTK and BCL2 inhibitors(ELSEVIER, 2022-01-25)The genomic landscape of resistance to targeted agents (TAs) used as monotherapy in chronic lymphocytic leukemia (CLL) is complex and often heterogeneous at the patient level. To gain insight into the clonal architecture of acquired genomic resistance to Bruton tyrosine kinase (BTK) inhibitors and B-cell lymphoma 2 (BCL2) inhibitors in CLL, particularly in patients carrying multiple resistance mutations, we performed targeted single-cell DNA sequencing of 8 patients who developed progressive disease (PD) on TAs (either class). In all cases, analysis of single-cell architecture revealed mutual exclusivity between multiple resistance mutations to the same TA class, variable clonal co-occurrence of multiple mutations affecting different TAs in patients exposed to both classes, and a phenomenon of multiple independent emergences of identical nucleotide changes leading to canonical resistance mutations. We also report the first observation of established BCL2 resistance mutations in a patient with mantle cell lymphoma (MCL) following PD on sequential monotherapy, implicating BCL2 as a venetoclax resistance mechanism in MCL. Taken together, these data reveal the significant clonal complexity of CLL and MCL progression on TAs at the nucleotide level and confirm the presence of multiple, clonally independent, mechanisms of TA resistance within each individual disease context.
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ItemPooled safety analysis of zanubrutinib monotherapy in patients with B-cell malignancies(ELSEVIER, 2022-02-22)Zanubrutinib is a selective Bruton tyrosine kinase (BTK) inhibitor evaluated in multiple B-cell malignancy studies. We constructed a pooled safety analysis to better understand zanubrutinib-associated treatment-emergent adverse events (TEAEs) and identify treatment-limiting toxicities. Data were pooled from 6 studies (N = 779). Assessments included type, incidence, severity, and outcome of TEAEs. Median age was 65 years; 20% were ≥75 years old. Most patients had Waldenström macroglobulinemia (33%), chronic lymphocytic leukemia/small lymphocytic lymphoma (29%), or mantle-cell lymphoma (19%). Median treatment duration was 26 months (range, 0.1-65); 16% of patients were treated for ≥3 years. Common nonhematologic TEAEs were upper respiratory tract infection (URI, 39%), rash (27%), bruising (25%), musculoskeletal pain (24%), diarrhea (23%), cough (21%), pneumonia (21%), urinary tract infection (UTI), and fatigue (15% each). Most common grade ≥3 TEAEs were pneumonia (11%), hypertension (5%), URI, UTI, sepsis, diarrhea, and musculoskeletal pain (2% each). Atrial fibrillation and major hemorrhage occurred in 3% and 4% of patients, respectively. Atrial fibrillation, hypertension, and diarrhea occurred at lower rates than those reported historically for ibrutinib. Grade ≥3 adverse events included neutropenia (23%), thrombocytopenia (8%), and anemia (8%). Serious TEAEs included pneumonia (11%), sepsis (2%), and pyrexia (2%).Treatment discontinuations and dose reductions for adverse events occurred in 10% and 8% of patients, respectively. Thirty-nine patients (4%) had fatal TEAEs, including pneumonia (n = 9), sepsis (n = 4), unspecified cause (n = 4), and multiple organ dysfunction syndrome (n = 5). This analysis demonstrates that zanubrutinib is generally well tolerated with a safety profile consistent with known BTK inhibitor toxicities; these were manageable and mostly reversible.
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ItemPredictors of Chronic Opioid Use: A Population-Level Analysis of North Carolina Cancer Survivors Using Multi-Payer Claims.(Oxford University Press (OUP), 2021-11-02)BACKGROUND: No population-based studies have examined chronic opioid use among cancer survivors who are diverse with respect to diagnosis, age group, and insurance status. METHODS: We conducted a retrospective cohort study using North Carolina cancer registry data linked with claims from public and private insurance (2006-2016). We included adults with nonmetastatic cancer who had no prior chronic opioid use (n = 38 366). We used modified Poisson regression to assess the adjusted relative risk of chronic opioid use in survivorship (>90-day continuous supply of opioids in the 13-24 months following diagnosis) associated with patient characteristics. RESULTS: Only 3.0% of cancer survivors in our cohort used opioids chronically in survivorship. Predictors included younger age (adjusted risk ratio [aRR] 50-59 vs 60-69 = 1.23, 95% confidence interval [CI] = 1.05 to 1.43), baseline depression (aRR = 1.22, 95% CI = 1.06 to 1.41) or substance use (aRR = 1.43, 95% CI = 1.15 to 1.78) and Medicaid (aRR vs private = 1.93, 95% CI = 1.56 to 2.40). Survivors who used opioids intermittently (vs not at all) before diagnosis were twice as likely to use opioids chronically in survivorship (aRR = 2.62, 95% CI = 2.28 to 3.02). Those who used opioids chronically (vs intermittently or not at all) during active treatment had a nearly 17-fold increased likelihood of chronic use in survivorship (aRR = 16.65, 95% CI = 14.30 to 19.40). CONCLUSIONS: Younger and low-income survivors, those with baseline depression or substance use, and those who require chronic opioid therapy during treatment are at increased risk for chronic opioid use in survivorship. Our findings point to opportunities to improve assessment of psychosocial histories and to engage patients in shared decision-making around long-term pain management, when chronic opioid therapy is required during treatment.
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ItemComprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing(BMC, 2021-11-11)A modified Chromium 10x droplet-based protocol that subsamples cells for both short-read and long-read (nanopore) sequencing together with a new computational pipeline (FLAMES) is developed to enable isoform discovery, splicing analysis, and mutation detection in single cells. We identify thousands of unannotated isoforms and find conserved functional modules that are enriched for alternative transcript usage in different cell types and species, including ribosome biogenesis and mRNA splicing. Analysis at the transcript level allows data integration with scATAC-seq on individual promoters, improved correlation with protein expression data, and linked mutations known to confer drug resistance to transcriptome heterogeneity.