Transcription elongation defects link oncogenic SF3B1 mutations to targetable alterations in chromatin landscape.

Transcription and splicing of pre-messenger RNA are closely coordinated, but how this functional coupling is disrupted in human diseases remains unexplored. Using isogenic cell lines, patient samples, and a mutant mouse model, we investigated how cancer-associated mutations in SF3B1 alter transcription. We found that these mutations reduce the elongation rate of RNA polymerase II (RNAPII) along gene bodies and its density at promoters. The elongation defect results from disrupted pre-spliceosome assembly due to impaired protein-protein interactions of mutant SF3B1. The decreased promoter-proximal RNAPII density reduces both chromatin accessibility and H3K4me3 marks at promoters. Through an unbiased screen, we identified epigenetic factors in the Sin3/HDAC/H3K4me pathway, which, when modulated, reverse both transcription and chromatin changes. Our findings reveal how splicing factor mutant states behave functionally as epigenetic disorders through impaired transcription-related changes to the chromatin landscape. We also present a rationale for targeting the Sin3/HDAC complex as a therapeutic strategy.

PD-1H/VISTA mediates immune evasion in acute myeloid leukemia.

Acute myeloid leukemia (AML) presents a pressing medical need in that it is largely resistant to standard chemotherapy as well as modern therapeutics, such as targeted therapy and immunotherapy, including anti-programmed cell death protein (anti-PD) therapy. We demonstrate that programmed death-1 homolog (PD-1H), an immune coinhibitory molecule, is highly expressed in blasts from the bone marrow of AML patients, while normal myeloid cell subsets and T cells express PD-1H. In studies employing syngeneic and humanized AML mouse models, overexpression of PD-1H promoted the growth of AML cells, mainly by evading T cell-mediated immune responses. Importantly, ablation of AML cell-surface PD-1H by antibody blockade or genetic knockout significantly inhibited AML progression by promoting T cell activity. In addition, the genetic deletion of PD-1H from host normal myeloid cells inhibited AML progression, and the combination of PD-1H blockade with anti-PD therapy conferred a synergistic antileukemia effect. Our findings provide the basis for PD-1H as a potential therapeutic target for treating human AML.

Breakthrough invasive fungal infections on isavuconazole prophylaxis in hematologic malignancy & hematopoietic stem cell transplant patients.

BACKGROUND: Isavuconazole (ISA) is a newer antifungal used in patients with history of hematologic malignancies and hematopoietic transplant and cellular therapies (HM/TCT). Although it has a more favorable side-effect profile, breakthrough invasive fungal infections (bIFIs) while on ISA have been reported. METHODS: In this single-center retrospective study evaluating HM/TCT patients who received prophylactic ISA for ≥7 days, we evaluated the incidence and potential risk factors for bIFIs. RESULTS: We evaluated 106 patients who received prophylactic ISA. The patients were predominantly male (60.4%) with median age of 65 (range: 21-91) years. Acute myeloid leukemia (48/106, 45.3%) was the most common HM, with majority having relapsed and/or refractory disease (43/106, 40.6%) or receiving ongoing therapy (38/106, 35.8%). Nineteen patients (17.9%) developed bIFIs-nine proven [Fusarium (3), Candida (2), Mucorales plus Aspergillus (2), Mucorales (1), Colletotrichum (1)], four probable invasive pulmonary Aspergillus, and six possible infections. Twelve patients were neutropenic for a median of 28 (8-253) days prior to bIFI diagnosis. ISA levels checked within 7 days of bIFI diagnosis (median: 3.65 µg/mL) were comparable to industry-sponsored clinical trials. All-cause mortality among the bIFI cases was 47.4% (9/19).We also noted clinically significant cytomegalovirus co-infection in 5.3% (1/19). On univariate analysis, there were no significant differences in baseline comorbidities and potential risk factors between the two groups. CONCLUSION: ISA prophylaxis was associated with a significant cumulative incidence of bIFIs. Despite the appealing side-effect and drug-interaction profile of ISA, clinicians must be vigilant about the potential risk for bIFIs.

Transcription elongation defects link oncogenic splicing factor mutations to targetable alterations in chromatin landscape.

Transcription and splicing of pre-messenger RNA are closely coordinated, but how this functional coupling is disrupted in human disease remains unexplored. Here, we investigated the impact of non-synonymous mutations in SF3B1 and U2AF1, two commonly mutated splicing factors in cancer, on transcription. We find that the mutations impair RNA Polymerase II (RNAPII) transcription elongation along gene bodies leading to transcription-replication conflicts, replication stress and altered chromatin organization. This elongation defect is linked to disrupted pre-spliceosome assembly due to impaired association of HTATSF1 with mutant SF3B1. Through an unbiased screen, we identified epigenetic factors in the Sin3/HDAC complex, which, when modulated, normalize transcription defects and their downstream effects. Our findings shed light on the mechanisms by which oncogenic mutant spliceosomes impact chromatin organization through their effects on RNAPII transcription elongation and present a rationale for targeting the Sin3/HDAC complex as a potential therapeutic strategy. HIGHLIGHTS: Oncogenic mutations of SF3B1 and U2AF1 cause a gene-body RNAPII elongation defectRNAPII transcription elongation defect leads to transcription replication conflicts, DNA damage response, and changes to chromatin organization and H3K4me3 marksThe transcription elongation defect is linked to disruption of the early spliceosome formation through impaired interaction of HTATSF1 with mutant SF3B1.Changes to chromatin organization reveal potential therapeutic strategies by targeting the Sin3/HDAC pathway.

Tracking the evolution of therapy-related myeloid neoplasms using chemotherapy signatures.

Patients treated with cytotoxic therapies, including autologous stem cell transplantation, are at risk for developing therapy-related myeloid neoplasms (tMN). Preleukemic clones (ie, clonal hematopoiesis [CH]) are detectable years before the development of these aggressive malignancies, although the genomic events leading to transformation and expansion are not well defined. Here, by leveraging distinctive chemotherapy-associated mutational signatures from whole-genome sequencing data and targeted sequencing of prechemotherapy samples, we reconstructed the evolutionary life-history of 39 therapy-related myeloid malignancies. A dichotomy was revealed, in which neoplasms with evidence of chemotherapy-induced mutagenesis from platinum and melphalan were hypermutated and enriched for complex structural variants (ie, chromothripsis), whereas neoplasms with nonmutagenic chemotherapy exposures were genomically similar to de novo acute myeloid leukemia. Using chemotherapy-associated mutational signatures as temporal barcodes linked to discrete clinical exposure in each patient's life, we estimated that several complex events and genomic drivers were acquired after chemotherapy was administered. For patients with prior multiple myeloma who were treated with high-dose melphalan and autologous stem cell transplantation, we demonstrate that tMN can develop from either a reinfused CH clone that escapes melphalan exposure and is selected after reinfusion, or from TP53-mutant CH that survives direct myeloablative conditioning and acquires melphalan-induced DNA damage. Overall, we revealed a novel mode of tMN progression that is not reliant on direct mutagenesis or even exposure to chemotherapy. Conversely, for tMN that evolve under the influence of chemotherapy-induced mutagenesis, distinct chemotherapies not only select preexisting CH but also promote the acquisition of recurrent genomic drivers.

Molecular characteristics and outcomes in Hispanic and non-Hispanic patients with acute myeloid leukemia.

Hispanic patients have been reported to have an increased incidence of AML and possibly inferior outcomes compared to non-Hispanics. We conducted a retrospective study of 225 AML patients (58 Hispanic and 167 non-Hispanic) at two academic medical centers in Florida. Disease characteristics, cytogenetics, mutation profiles, and clinical outcomes were assessed. Hispanic patients were younger at presentation than non-Hispanics (p = 0.0013). We found associations between single gene mutations and ethnicity, with IDH1 mutations being more common in non-Hispanics (95.2% vs. 4.8%, p = 0.0182) and WT1 mutations more common in Hispanics (62.5% vs. 37.5%, p = 0.0455). We also found an emerging trend towards adverse risk cytogenetics in Hispanic patients (p = 0.1796), as well as high risk fusions such as MLL-r (70% vs. 30%, p = 0.004). There was no difference in overall survival (OS) between Hispanic and non-Hispanics patients. When examining only newly diagnosed patients (n = 105), there was improved OS in Hispanics (median 44.7 months vs. 14 months, p = 0.026) by univariate analysis and equivalent OS by multivariate analysis (hazard ratio = 1.52 [95% CI = 0.74-3.15]). Hispanics with a driver mutation not class-defining had improved survival compared to non-Hispanics. Our study demonstrates significant genetic differences between Floridian Hispanics and non-Hispanics, but no difference in OS in patients treated at an academic medical center.

What constitutes meaningful improvement in myelodysplastic syndromes?

Myelodysplastic syndromes (MDS) are a heterogeneous spectrum of clonal stem cell disorders characterized by ineffective hematopoiesis and resulting peripheral blood cytopenias. Clinical manifestations of the disorder are varied and range from mild asymptomatic anemia to a markedly truncated life expectancy, underscoring the importance of risk-adapted therapy. MDS therapy for both lower- and higher-risk patients is an area of immense therapeutic opportunity. This is partly due to the diversity of treatment goals between patients and defining what constitutes meaningful benefit from a patient's viewpoint. Correlating metrics such as hematologic improvement or response rate to develop novel therapies can be falsely reassuring to physicians and patients, specifically if the interventions are burdensome, disconnected from a patient's sense of wellbeing and do not correlate with an improvement in quality of life or longevity. We discuss aligning drug development goals with patient goals that will lead to meaningful improvement in MDS clinical care.

Peripheral Blood Involvement at Staging in Patients With Aggressive Peripheral T-Cell Lymphoma.

INTRODUCTION: Peripheral T-Cell Lymphomas (PTCL) are a rare subgroup of lymphomas with a poor outcome.Traditional prognostic measures rely heavily on disease stage, and with the advent of targeted treatment, further stratificationcriteria are needed to guide treatment. To date, the impact of blood involvement at diagnosis on outcomes has not been assessed. MATERIALS AND METHODS: We retrospectively reviewed blood involvement by flow cytometry at diagnosis in 102 consecutivelytreated patients who had flow cytometry data available at diagnosis. Of these, 78 patients with nodal subtypes were identified andstudied in this analysis. RESULTS: Of 78 patients with nodal subtypes of PTCL who had flow data available at the time ofdiagnosis, circulating populations of malignant T cells matching those in the biopsied lymph nodes were found in 21 patients bymultiparameter flow cytometry. A positive flow cytometry was highly correlated with bone marrow involvement. The patientswith a negative flow cytometry had a trend toward a longer median PFS compared to those with a positive flow but there was noimpact on overall survival. CONCLUSIONS: Circulating malignant tumor cells can be found in the peripheral blood in a subset ofpatients with aggressive nodal T-cell lymphomas, including peripheral t-cell lymphoma not otherwise specified andangioimmunoblastic T-cell lymphomas, and blood involvement is correlated with bone marrow involvement.

In vivo anti-tumor effect of PARP inhibition in IDH1/2 mutant MDS/AML resistant to targeted inhibitors of mutant IDH1/2.

Treatment options for patients with relapsed/refractory acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS) are scarce. Recurring mutations, such as mutations in isocitrate dehydrogenase-1 and -2 (IDH1/2) are found in subsets of AML and MDS, are therapeutically targeted by mutant enzyme-specific small molecule inhibitors (IDHmi). IDH mutations induce diverse metabolic and epigenetic changes that drive malignant transformation. IDHmi alone are not curative and resistance commonly develops, underscoring the importance of alternate therapeutic options. We were first to report that IDH1/2 mutations induce a homologous recombination (HR) defect, which confers sensitivity to poly (ADP)-ribose polymerase inhibitors (PARPi). Here, we show that the PARPi olaparib is effective against primary patient-derived IDH1/2-mutant AML/ MDS xeno-grafts (PDXs). Olaparib efficiently reduced overall engraftment and leukemia-initiating cell frequency as evident in serial transplantation assays in IDH1/2-mutant but not -wildtype AML/MDS PDXs. Importantly, we show that olaparib is effective in both IDHmi-naïve and -resistant AML PDXs, critical given the high relapse and refractoriness rates to IDHmi. Our pre-clinical studies provide a strong rationale for the translation of PARP inhibition to patients with IDH1/2-mutant AML/ MDS, providing an additional line of therapy for patients who do not respond to or relapse after targeted mutant IDH inhibition.

Advances in non-intensive chemotherapy treatment options for adults diagnosed with acute myeloid leukemia.

Acute myeloid leukemia (AML) is primarily a disease of older adults. Many older patients with AML are not candidates for intensive chemotherapy regimens aimed at inducing remission before transplantation. The prognosis for this patient population remains poor, with 5-year overall survival (OS) rates of less than 10 %. At present, there is no standard of care, and clinical trials should be considered. Hypomethylating agents often are the mainstay of treatment in this setting; however, improved genetic profiling and risk stratification based on molecular, biological, and clinical characteristics of AML enhance the ability to identify an individual patient's risk and can refine therapeutic options. Over the past 2 years, several novel agents have been approved for AML patients in either the frontline or relapsed settings. Additional agents have also shown promising activity. It is becoming a challenge for physicians to navigate these different options and select the optimal therapy or combination of therapies. The aim of this review is to summarize the available information to assist with treatment decisions for leukemia patients who are not suitable for intensive chemotherapy.

Hypomethylating agent based combinations in higher risk myelodysplastic syndrome.

For over a decade the hypomethylating agents (HMA) azacitidine and decitabine have been the mainstay of therapy for myelodysplastic syndrome (MDS). There is a critical need to improve frontline therapy, given that only up to half of high-risk MDS patients will respond to HMA therapy, and responses are short-lived. Currently, a key strategy has been to combine HMAs with other novel agents to improve patient outcomes. While synergy of agents is the goal of combination therapy, combinations often come at the cost of increased side effects that are often intolerable in this vulnerable population. The purpose of this review is to critically examine clinically relevant HMA combinations and discuss the future of MDS management.

Insights into novel emerging epigenetic drugs in myeloid malignancies.

Epigenetics has been defined as 'a stably heritable phenotype resulting from changes in a chromosome without alterations in the DNA sequence' and several epigenetic regulators are recurrently mutated in hematological malignancies. Epigenetic modifications include changes such as DNA methylation, histone modifications and RNA associated gene silencing. Transcriptional regulation, chromosome stability, DNA replication and DNA repair are all controlled by these modifications. Mutations in genes encoding epigenetic modifiers are a frequent occurrence in hematologic malignancies and important in both the initiation and progression of cancer. Epigenetic modifications are also frequently reversible, allowing excellent opportunities for therapeutic intervention. The goal of epigenetic therapies is to reverse epigenetic dysregulation, restore the epigenetic balance, and revert malignant cells to a more normal condition. The role of epigenetic therapies thus far is most established in hematologic malignancies, with several agents already approved by the US Food and Drug Administration. In this review, we discuss pharmacological agents targeting epigenetic regulators.

What are the most promising new agents in myelodysplastic syndromes?

PURPOSE OF REVIEW: Myelodysplastic syndromes (MDS) are a diverse group of clonal disorders of hematopoietic stem or progenitor cells that represent the most common class of acquired bone marrow failure syndromes in adults. Despite significant improvement in the pathologic insight into this group of disorders, therapeutic options remain limited and allogeneic hematopoietic stem-cell transplantation is the only treatment that can induce long-term remission in patients with MDS. The goals of therapy for MDS are based on disease prognostication, with a focus of minimizing transfusion dependence and preserving quality of life in low-risk groups and preventing progression of disease to acute myeloid leukemia in high-risk groups. Given the dearth of approved treatment options, there is a marked need for novel therapies across the board, and there are several novel agents currently in the pipeline. RECENT FINDINGS: Among the promising agents with preclinical and early phase efficacy in higher risk MDS, apoptosis targeting with BCL-2 inhibitors have been a standout. There is also a keen interest in immunotherapy, and targeted agents (genetic, signaling pathways, bispecific antibodies, antibody-drug conjugates, and others described in this review). SUMMARY: In this review, we will highlight some of the promising new agents currently under investigation for the management of MDS.

Updates on the use of neoadjuvant therapy in borderline resectable pancreatic cancer.

Pancreatic cancer is an aggressive and devastating cancer that continues to have high 5-year mortality rates despite advancements in the field. Surgery remains the only curative treatment; however, most patients present with late stage disease deemed unresectable. By refining the resection guidelines to include a borderline resectable group, as well as advancements in neoadjuvant chemotherapy and radiation that improve resectability, we may improve upon outcomes for patients with more invasive disease. Here we summarize and discuss findings presented at the 2014 ASCO Gastrointestinal Cancers Symposium (Abstracts #283, #302, #309, #274, #275, #327) that relate neoadjuvant therapeutic strategies and borderline resectable cancers.

A little CIN may cost a lot: revisiting aneuploidy and cancer.

Despite over 100 years of study, the role of aneuploidy in cancer remains poorly understood. This review highlights the advances in understanding the causes and consequences of aneuploidy. Recent work has illuminated ways in which aneuploidy could have either tumor-promoting or tumor-suppressing effects, similar to what is known for other forms of genetic instability such as telomere attrition [Maser RS, DePinho RA: Connecting chromosomes, crisis, and cancer. Science 2002, 297:565-569]. We explore the possibility that aneuploidy could be just another type of 'mutation', with potential beneficial and deleterious effects, depending on the chromosomes involved and the specific selective pressures the cells experience. We also discuss the potential therapeutic implications of changes in physiology associated with aneuploidy.

Mechanisms to suppress multipolar divisions in cancer cells with extra centrosomes.

Multiple centrosomes in tumor cells create the potential for multipolar divisions that can lead to aneuploidy and cell death. Nevertheless, many cancer cells successfully divide because of mechanisms that suppress multipolar mitoses. A genome-wide RNAi screen in Drosophila S2 cells and a secondary analysis in cancer cells defined mechanisms that suppress multipolar mitoses. In addition to proteins that organize microtubules at the spindle poles, we identified novel roles for the spindle assembly checkpoint, cortical actin cytoskeleton, and cell adhesion. Using live cell imaging and fibronectin micropatterns, we found that interphase cell shape and adhesion pattern can determine the success of the subsequent mitosis in cells with extra centrosomes. These findings may identify cancer-selective therapeutic targets: HSET, a normally nonessential kinesin motor, was essential for the viability of certain extra centrosome-containing cancer cells. Thus, morphological features of cancer cells can be linked to unique genetic requirements for survival.