Benefits for children with suspected cancer from routine whole-genome sequencing.

Clinical whole-genome sequencing (WGS) has been shown to deliver potential benefits to children with cancer and to alter treatment in high-risk patient groups. It remains unknown whether offering WGS to every child with suspected cancer can change patient management. We collected WGS variant calls and clinical and diagnostic information from 281 children (282 tumors) across two English units (n = 152 from a hematology center, n = 130 from a solid tumor center) where WGS had become a routine test. Our key finding was that variants uniquely attributable to WGS changed the management in ~7% (20 out of 282) of cases while providing additional disease-relevant findings, beyond standard-of-care molecular tests, in 108 instances for 83 (29%) cases. Furthermore, WGS faithfully reproduced every standard-of-care molecular test (n = 738) and revealed several previously unknown genomic features of childhood tumors. We show that WGS can be delivered as part of routine clinical care to children with suspected cancer and can change clinical management by delivering unexpected genomic insights. Our experience portrays WGS as a clinically impactful assay for routine practice, providing opportunities for assay consolidation and for delivery of molecularly informed patient care.

Introduction and impact of routine whole genome sequencing in the diagnosis and management of sarcoma.

BACKGROUND: Sarcomas are diverse neoplasms with highly variable histological appearances in which diagnosis is often challenging and management options for metastatic/unresectable disease limited. Many sarcomas have distinctive molecular alterations, but the range of alterations is large, variable in type and rapidly increasing, meaning that testing by limited panels is unable to capture the broad spectrum of clinically pertinent genomic drivers required. Paired whole genome sequencing (WGS) in contrast allows comprehensive assessment of small variants, copy number and structural variants along with mutational signature analysis and germline testing. METHODS: Introduction of WGS as a diagnostic standard for all eligible patients with known or suspected soft tissue sarcoma over a 2-year period at a soft tissue sarcoma treatment centre. RESULTS: WGS resulted in a refinement in the diagnosis in 37% of cases, identification of a target for personalised therapy in 33% of cases, and a germline alteration in 4% of cases. CONCLUSION: Introduction of WGS poses logistical and training challenges, but offers significant benefits to this group of patients.

PI3Kγ maintains the self-renewal of acute myeloid leukemia stem cells by regulating the pentose phosphate pathway.

ABSTRACT: Acute myeloid leukemia (AML) is an aggressive hematological malignancy originating from transformed hematopoietic stem or progenitor cells. AML prognosis remains poor owing to resistance and relapse driven by leukemia stem cells (LSCs). Targeting molecules essential for LSC function is a promising therapeutic approach. The phosphatidylinositol 3-kinase (PI3K)/AKT pathway is often dysregulated in AML. We found that although PI3Kγ is highly enriched in LSCs and critical for self-renewal, it was dispensable for normal hematopoietic stem cells. Mechanistically, PI3Kγ-AKT signaling promotes nuclear factor erythroid 2-related factor 2 (NRF2) nuclear accumulation, which induces 6-phosphogluconate dehydrogenase (PGD) and the pentose phosphate pathway, thereby maintaining LSC stemness. Importantly, genetic or pharmacological inhibition of PI3Kγ impaired expansion and stemness of murine and human AML cells in vitro and in vivo. Together, our findings reveal a key role for PI3Kγ in selectively maintaining LSC function by regulating AKT-NRF2-PGD metabolic pathway. Targeting the PI3Kγ pathway may, therefore, eliminate LSCs without damaging normal hematopoiesis, providing a promising therapeutic strategy for AML.

Preventing Future Harm: Identifying the Drivers of an Unsafe Discharge to Improve Safety on an Inpatient Oncology Service.

Cancer Morbidity, Mortality, and Improvement Rounds is a series of articles intended to explore the unique safety risks experienced by oncology patients through the lens of quality improvement, systems and human factors engineering, and cognitive psychology. For purposes of clarity, each case focuses on a single theme, although, as is true for all medical incidents, there are almost always multiple, overlapping, contributing factors. The quality improvement paradigm used here, which focuses on root cause analyses and opportunities to improve care delivery systems, was previously outlined in this journal.This article describes the care of a young patient with aggressive breast cancer, declining performance status, and multiple hospital admissions who died shortly after being discharged home without essential medications or an adequate plan for follow-up. The patient's death due to her malignancy was unavoidable, but she had inadequate resources before her death, leading to avoidable suffering. This outcome resulted from a series of minor errors attributable to inadequate handoffs, challenges establishing realistic goals of care, and hierarchy within and between medical teams that resulted in major lapses at the time of discharge. We explore these issues and discuss how this case led to the establishment of programs designed to empower health care providers and increase engagement of outpatient oncologists at critical points of patients' disease courses.

PI3Kß controls immune evasion in PTEN-deficient breast tumours.

Loss of the PTEN tumour suppressor is one of the most common oncogenic drivers across all cancer types1. PTEN is the major negative regulator of PI3K signalling. The PI3Kß isoform has been shown to play an important role in PTEN-deficient tumours, but the mechanisms underlying the importance of PI3Kß activity remain elusive. Here, using a syngeneic genetically engineered mouse model of invasive breast cancer driven by ablation of both Pten and Trp53 (which encodes p53), we show that genetic inactivation of PI3Kß led to a robust anti-tumour immune response that abrogated tumour growth in syngeneic immunocompetent mice, but not in immunodeficient mice. Mechanistically, PI3Kß inactivation in the PTEN-null setting led to reduced STAT3 signalling and increased the expression of immune stimulatory molecules, thereby promoting anti-tumour immune responses. Pharmacological PI3Kß inhibition also elicited anti-tumour immunity and synergized with immunotherapy to inhibit tumour growth. Mice with complete responses to the combined treatment displayed immune memory and rejected tumours upon re-challenge. Our findings demonstrate a molecular mechanism linking PTEN loss and STAT3 activation in cancer and suggest that PI3Kß controls immune escape in PTEN-null tumours, providing a rationale for combining PI3Kß inhibitors with immunotherapy for the treatment of PTEN-deficient breast cancer.

Practice-Level Variation in Molecular Testing and Use of Targeted Therapy for Patients With Non-Small Cell Lung Cancer and Colorectal Cancer.

Importance: All patients with newly diagnosed non-small cell lung cancer (NSCLC) and colorectal cancer (CRC) should receive molecular testing to identify those who can benefit from targeted therapies. However, many patients do not receive recommended testing and targeted therapies. Objective: To compare rates of molecular testing and targeted therapy use by practice type and across practices. Design, Setting, and Participants: This cross-sectional study used 100% Medicare fee-for-service data from 2015 through 2019 to identify beneficiaries with new metastatic NSCLC or CRC diagnoses receiving systemic therapy and to assign patients to oncology practices. Hierarchical linear models were used to characterize variation by practice type and across practices. Data analysis was conducted from June 2019 to October 2022. Exposures: Oncology practice providing care. Outcomes: Primary outcomes were rates of molecular testing and targeted therapy use for patients with NSCLC and CRC. Secondary outcomes were rates of multigene testing for NSCLC and CRC. Results: There were 106 228 Medicare beneficiaries with incident NSCLC (31 521 [29.7%] aged 65-69 years; 50 348 [47.4%] female patients; 2269 [2.1%] Asian, 8282 [7.8%] Black, and 91 215 [85.9%] White patients) and 39 512 beneficiaries with incident CRC (14 045 [35.5%] aged 65-69 years; 17 518 [44.3%] female patients; 896 [2.3%] Asian, 3521 [8.9%] Black, and 32 753 [82.9%] White patients) between 2015 and 2019. Among these beneficiaries, 18 435 (12.9%) were treated at National Cancer Institute (NCI)-designated centers, 8187 (5.6%) were treated at other academic centers, and 94 329 (64.7%) were treated at independent oncology practices. Molecular testing rates increased from 74% to 85% for NSCLC and 45% to 65% for CRC. First-line targeted therapy use decreased from 12% to 8% among patients with NSCLC and was constant at 5% for patients with CRC. For NSCLC, molecular testing rates were similar across practice types while rates of multigene panel use (13.2%) and targeted therapy use (16.6%) were highest at NCI-designated cancer centers. For CRC, molecular testing rates were 3.8 (95% CI: 1.2-6.5), 3.3 (95% CI, 0.4-6.1), and 12.2 (95% CI, 9.1-15.3) percentage points lower at hospital-owned practices, large independent practices, and small independent practices, respectively. Rates of targeted therapy use for CRC were similar across practice types. After adjusting for patient characteristics, there was moderate variation in molecular testing and targeted therapy use across oncology practices. Conclusions and Relevance: In this cross-sectional study of Medicare beneficiaries, molecular testing rates for NSCLC and CRC increased in recent years but remained lower than recommended levels. Rates of targeted therapy use decreased for NSCLC and remained stable for CRC. Variation across practices suggests that where a patient was treated may have affected access to recommended testing and efficacious treatments.

STING agonism overcomes STAT3-mediated immunosuppression and adaptive resistance to PARP inhibition in ovarian cancer.

BACKGROUND: Poly (ADP-ribose) polymerase (PARP) inhibition (PARPi) has demonstrated potent therapeutic efficacy in patients with BRCA-mutant ovarian cancer. However, acquired resistance to PARPi remains a major challenge in the clinic. METHODS: PARPi-resistant ovarian cancer mouse models were generated by long-term treatment of olaparib in syngeneic Brca1-deficient ovarian tumors. Signal transducer and activator of transcription 3 (STAT3)-mediated immunosuppression was investigated in vitro by co-culture experiments and in vivo by analysis of immune cells in the tumor microenvironment (TME) of human and mouse PARPi-resistant tumors. Whole genome transcriptome analysis was performed to assess the antitumor immunomodulatory effect of STING (stimulator of interferon genes) agonists on myeloid cells in the TME of PARPi-resistant ovarian tumors. A STING agonist was used to overcome STAT3-mediated immunosuppression and acquired PARPi resistance in syngeneic and patient-derived xenografts models of ovarian cancer. RESULTS: In this study, we uncover an adaptive resistance mechanism to PARP inhibition mediated by tumor-associated macrophages (TAMs) in the TME. Markedly increased populations of protumor macrophages are found in BRCA-deficient ovarian tumors that rendered resistance to PARPi in both murine models and patients. Mechanistically, PARP inhibition elevates the STAT3 signaling pathway in tumor cells, which in turn promotes protumor polarization of TAMs. STAT3 ablation in tumor cells mitigates polarization of protumor macrophages and increases tumor-infiltrating T cells on PARP inhibition. These findings are corroborated in patient-derived, PARPi-resistant BRCA1-mutant ovarian tumors. Importantly, STING agonists reshape the immunosuppressive TME by reprogramming myeloid cells and overcome the TME-dependent adaptive resistance to PARPi in ovarian cancer. This effect is further enhanced by addition of the programmed cell death protein-1 blockade. CONCLUSIONS: We elucidate an adaptive immunosuppression mechanism rendering resistance to PARPi in BRCA1-mutant ovarian tumors. This is mediated by enrichment of protumor TAMs propelled by PARPi-induced STAT3 activation in tumor cells. We also provide a new strategy to reshape the immunosuppressive TME with STING agonists and overcome PARPi resistance in ovarian cancer.

Variation in Use of Lung Cancer Targeted Therapies Across State Medicaid Programs, 2020-2021.

Importance: Targeted therapies for EGFR (OMIM 131550)- and ALK (OMIM 105590)-altered metastatic non-small cell lung cancer (NSCLC) substantially improve outcomes for some patients. However, use of these therapies is lower among Medicaid patients, and access to oncology care varies across state Medicaid programs. Evidence is lacking on how use of targeted therapies for metastatic NSCLC varies across state Medicaid programs. Objectives: To characterize state-level variation in the use of targeted therapies among Medicaid patients with metastatic NSCLC and to describe factors associated with this variation. Design, Setting, and Participants: This cross-sectional study used publicly available data from the Medicaid Drug Utilization Database from 2020 and 2021 and peer-reviewed data on NSCLC incidence, the prevalence of EGFR and ALK alterations, and expected treatment durations to estimate expected use of targeted therapies for EGFR- and ALK-altered NSCLC in 33 states. Exposures: State-specific Medicaid programs and state policies and characteristics. Main Outcomes and Measures: The primary outcome was the estimated proportion of person-time of Medicaid patients with EGFR- or ALK-altered NSCLC associated with receipt of targeted therapy in each state Medicaid program. Nested linear regression models examined associations between the observed variation and state policies and characteristics. Results: There were an estimated 3461 person-years in which EGFR- and ALK-targeted therapies were indicated in 2020 and 2021. During these years, only 2281 person-years of EGFR- and ALK-targeted therapies were dispensed to Medicaid patients, suggesting that an estimated 66% of Medicaid patients with EGFR- and ALK-altered metastatic disease received indicated targeted therapies across all states. Rates of targeted therapy use ranged from 18% in Arkansas to 113% in Massachusetts; 30 of 33 states (91%) had lower rates of targeted therapy use than expected. The observed variation across state Medicaid programs was associated with Medicaid policies, the density of oncologists, and state gross domestic product per capita. Conclusions and Relevance: This study suggests that rates of targeted therapy use among Medicaid patients with EGFR- and ALK-altered NSCLC were lower than expected and varied across state Medicaid programs. State policies and characteristics were associated with the observed variation, indicating where interventions could improve access to treatment and outcomes for patients with NSCLC.

More than one route to render tumors resistant to cGAS/STING activation.

STING (stimulator of interferon genes) activation has considerable potential as a new strategy for cancer therapy, but clinical results have not been encouraging. Recent studies by Hong et al. and Li et al. explain why STING agonists often fail to regress human tumors and propose combinatorial strategies to overcome the protumor effects of STING activation.

Care Fragmentation, Faulty Communication, and Documentation Lapses Derail a Treatment Plan.

This is the second Cancer Morbidity, Mortality, and Improvement Rounds, a series of articles intended to explore the unique safety risks experienced by oncology patients through the lens of quality improvement, systems and human factors engineering, and cognitive psychology. This case describes the care of a patient who was diagnosed with locally advanced lung cancer during the COVID-19 pandemic; it highlights how gaps in communication and care coordination caused the patient to receive care that did not reflect the consensus of his multidisciplinary team. The discussion highlights the importance of multidisciplinary care, particularly for patients with stage III non-small-cell lung cancer, discusses factors that led to communication gaps, and examines how we should assign accountability across dispersed health care systems.Cancer Morbidity, Mortality, and Improvement Rounds is a series of articles intended to explore the unique safety risks experienced by oncology patients through the lens of quality improvement, systems and human factors engineering, and cognitive psychology. For purposes of clarity, each case focuses on a single theme, although, as is true for all medical incidents, there are almost always multiple, overlapping, contributing factors. The quality improvement paradigm used here, which focuses on root cause analyses and opportunities to improve care delivery systems, was previously outlined in this journal.

Non-uniform dystrophin re-expression after CRISPR-mediated exon excision in the dystrophin/utrophin double-knockout mouse model of DMD.

Duchenne muscular dystrophy (DMD) is the most prevalent inherited myopathy affecting children, caused by genetic loss of the gene encoding the dystrophin protein. Here we have investigated the use of the Staphylococcus aureus CRISPR-Cas9 system and a double-cut strategy, delivered using a pair of adeno-associated virus serotype 9 (AAV9) vectors, for dystrophin restoration in the severely affected dystrophin/utrophin double-knockout (dKO) mouse. Single guide RNAs were designed to excise Dmd exon 23, with flanking intronic regions repaired by non-homologous end joining. Exon 23 deletion was confirmed at the DNA level by PCR and Sanger sequencing, and at the RNA level by RT-qPCR. Restoration of dystrophin protein expression was demonstrated by western blot and immunofluorescence staining in mice treated via either intraperitoneal or intravenous routes of delivery. Dystrophin restoration was most effective in the diaphragm, where a maximum of 5.7% of wild-type dystrophin expression was observed. CRISPR treatment was insufficient to extend lifespan in the dKO mouse, and dystrophin was expressed in a within-fiber patchy manner in skeletal muscle tissues. Further analysis revealed a plethora of non-productive DNA repair events, including AAV genome integration at the CRISPR cut sites. This study highlights potential challenges for the successful development of CRISPR therapies in the context of DMD.

A Perfect Storm Averted: Flawed Systems, a Dropped Ball, and Cognitive Biases Delay a Critical Diagnosis.

This is the first case of Cancer Morbidity, Mortality, and Improvement Rounds, a series of articles intended to explore the unique safety risks experienced by oncology patients through the lens of quality improvement, systems and human factors engineering, and cognitive psychology. This case highlights how multiple overlapping factors contributed to a delay in diagnosing disseminated tuberculosis in a patient with lung cancer. The discussion focuses on the ways that cognitive biases contributed to the delayed diagnosis in a patient who, with the benefit of hindsight, exhibited several signs and symptoms suggesting tuberculosis.Cancer Morbidity, Mortality, and Improvement Rounds is a series of articles intended to explore the unique safety risks experienced by oncology patients through the lens of quality improvement, systems and human factors engineering, and cognitive psychology. For purposes of clarity, each case focuses on a single theme, although, as is true for all medical incidents, there are almost always multiple, overlapping, contributing factors. The quality improvement paradigm used here, which focuses on root cause analyses and opportunities to improve care delivery systems, was previously outlined in this journal.1.

The effects of thymoquinone on pancreatic cancer: Evidence from preclinical studies.

Thymoquinone (TQ) is a secondary metabolite found in abundance in very few plant species including Nigella sativa L., Monarda fistulosa L., Thymus vulgaris L. and Satureja montana L. Preclinical pharmacological studies have shown that TQ has many biological activities, such as anti-inflammatory, antioxidant and anticancer. Both in vivo and in vitro experiments have shown that TQ acts as an antitumor agent by altering cell cycle progression, inhibiting cell proliferation, stimulating apoptosis, inhibiting angiogenesis, reducing metastasis and affecting autophagy. In this comprehensive study, the evidence on the pharmacological potential of TQ on pancreatic cancer is reviewed. The positive results of preclinical studies support the view that TQ can be considered as an additional therapeutic agent against pancreatic cancer. The possibilities of success for this compound in human medicine should be further explored through clinical trials.

AR cooperates with SMAD4 to maintain skeletal muscle homeostasis.

Androgens and androgen-related molecules exert a plethora of functions across different tissues, mainly through binding to the transcription factor androgen receptor (AR). Despite widespread therapeutic use and misuse of androgens as potent anabolic agents, the molecular mechanisms of this effect on skeletal muscle are currently unknown. Muscle mass in adulthood is mainly regulated by the bone morphogenetic protein (BMP) axis of the transforming growth factor (TGF)-ß pathway via recruitment of mothers against decapentaplegic homolog 4 (SMAD4) protein. Here we show that, upon activation, AR forms a transcriptional complex with SMAD4 to orchestrate a muscle hypertrophy programme by modulating SMAD4 chromatin binding dynamics and enhancing its transactivation activity. We challenged this mechanism of action using spinal and bulbar muscular atrophy (SBMA) as a model of study. This adult-onset neuromuscular disease is caused by a polyglutamine expansion (polyQ) in AR and is characterized by progressive muscle weakness and atrophy secondary to a combination of lower motor neuron degeneration and primary muscle atrophy. Here we found that the presence of an elongated polyQ tract impairs AR cooperativity with SMAD4, leading to an inability to mount an effective anti-atrophy gene expression programme in skeletal muscle in response to denervation. Furthermore, adeno-associated virus, serotype 9 (AAV9)-mediated muscle-restricted delivery of BMP7 is able to rescue the muscle atrophy in SBMA mice, supporting the development of treatments able to fine-tune AR-SMAD4 transcriptional cooperativity as a promising target for SBMA and other conditions associated with muscle loss.

STING agonism reprograms tumor-associated macrophages and overcomes resistance to PARP inhibition in BRCA1-deficient models of breast cancer.

PARP inhibitors (PARPi) have drastically changed the treatment landscape of advanced ovarian tumors with BRCA mutations. However, the impact of this class of inhibitors in patients with advanced BRCA-mutant breast cancer is relatively modest. Using a syngeneic genetically-engineered mouse model of breast tumor driven by Brca1 deficiency, we show that tumor-associated macrophages (TAMs) blunt PARPi efficacy both in vivo and in vitro. Mechanistically, BRCA1-deficient breast tumor cells induce pro-tumor polarization of TAMs, which in turn suppress PARPi-elicited DNA damage in tumor cells, leading to reduced production of dsDNA fragments and synthetic lethality, hence impairing STING-dependent anti-tumor immunity. STING agonists reprogram M2-like pro-tumor macrophages into an M1-like anti-tumor state in a macrophage STING-dependent manner. Systemic administration of a STING agonist breaches multiple layers of tumor cell-mediated suppression of immune cells, and synergizes with PARPi to suppress tumor growth. The therapeutic benefits of this combination require host STING and are mediated by a type I IFN response and CD8+ T cells, but do not rely on tumor cell-intrinsic STING. Our data illustrate the importance of targeting innate immune suppression to facilitate PARPi-mediated engagement of anti-tumor immunity in breast cancer.

Lessons for Oncology From the COVID-19 Pandemic: Operationalizing and Scaling Virtual Cancer Care in Health Systems.

ABSTRACT: After several decades of slow expansion, the use of virtual care in oncology rapidly expanded during the COVID-19 pandemic. Data from cancer centers across the country show that most patients and providers were satisfied with components of virtual care, and virtual care may be able to improve access to care. However, the rapid implementation of programs during the pandemic worsened disparities in access to virtual care. Health systems must develop strategies to monitor quality, support patients and providers, promote health equity, and overcome regulatory challenges to successfully deliver care in hybrid systems that combine in-person and virtual care.