Incidence of acute myeloid leukemia after breast cancer

NIAPU: network-informed adaptive positive-unlabeled learning for disease gene identification

MOTIVATION

Gene-disease associations are fundamental for understanding disease etiology and developing effective interventions and treatments. Identifying genes not yet associated with a disease due to a lack of studies is a challenging task in which prioritization based on prior knowledge is an important element. The computational search for new candidate disease genes may be eased by positive-unlabeled learning, the machine learning (ML) setting in which only a subset of instances are labeled as positive while the rest of the dataset is unlabeled. In this work, we propose a set of effective network-based features to be used in a novel Markov diffusion-based multi-class labeling strategy for putative disease gene discovery.

RESULTS

The performances of the new labeling algorithm and the effectiveness of the proposed features have been tested on 10 different disease datasets using three ML algorithms. The new features have been compared against classical topological and functional/ontological features and a set of network- and biological-derived features already used in gene discovery tasks. The predictive power of the integrated methodology in searching for new disease genes has been found to be competitive against state-of-the-art algorithms.

AVAILABILITY AND IMPLEMENTATION

The source code of NIAPU can be accessed at https://github.com/AndMastro/NIAPU. The source data used in this study are available online on the respective websites.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Risk of primary haematologic cancers following incident non-metastatic breast cancer: A Danish population-based cohort study

BACKGROUND

Breast cancer survivors may have increased risk of subsequent haematologic cancer. We compared their risk of haematologic cancers with the general population during 38 years of follow-up.

METHODS

Using population-based Danish medical registries, we assembled a nationwide cohort of women diagnosed with incident non-metastatic breast cancer during 1980-2017, with follow-up through 2018. We compared breast cancer survivors with the general population by computing standardised incidence ratios (SIR) and 95% confidence intervals (CI).

RESULTS

Among 101,117 breast cancer survivors, we observed 815 incident haematologic cancers (median follow-up: 7.9 years). We observed excess risk of acute myeloid leukaemia (AML) (SIR: 1.65, 95%CI: 1.33-2.01), particularly in women who received chemotherapy (SIR: 3.33, 95%CI: 2.24-4.75) and premenopausal women (SIR: 3.23, 95%CI: 2.41-4.25). The risk of acute lymphoid leukaemia (ALL) was increased (SIR: 2.25, 95%CI: 1.29-3.66), whereas the risk of chronic lymphoid leukaemia (CLL) was decreased (SIR: 0.66, 95%CI: 0.53-0.82). An additional analysis showed elevated risk of CLL 0-6 months after breast cancer diagnosis (SIR: 3.00 95%CI: 1.75-4.80).

CONCLUSION

Compared to the general population, breast cancer survivors had elevated risk of AML, particularly when treated with chemotherapy. The risk of ALL was elevated, whereas the risk of CLL was lower. The higher risk of CLL in the first six months after diagnosis likely reflects surveillance bias-due to intensified diagnostic efforts at breast cancer diagnosis and treatment-prompting earlier detection. This has likely reduced the long-term risk of CLL in breast cancer survivors.

Impact of Screening Mammography on Treatment in Young Women Diagnosed with Breast Cancer

BACKGROUND

There is little data exploring the impact of screening mammography on subsequent treatment in the 40-49-year age group with breast cancer. We sought to assess the association between frequency of mammography in young women and extent of surgery and chemotherapy required.

METHODS

An IRB-approved retrospective review was performed of patients diagnosed with breast cancer between ages 40 and 49 years from 1 January 2010 to 19 November 2018 within a single health system. Patients were grouped based on last screening 1-24 months prior to diagnosis (1-24 group), > 25 months prior to diagnosis (> 25 group), never screened, and > 25+ never screened (combination group). Multivariate logistic regression models were used to assess for associations between screening intervals and tumor and nodal stage, chemotherapy use, and extent of surgery.

RESULTS

Of 869 patients included for analysis, 20% were never screened, 60% screened 1-24 months, and 19% screened > 25 months prior to diagnosis. Compared with the 1-24 months group, the never-screened group, > 25 months group, and combined group were more likely to receive chemotherapy. The never-screened and combined groups were more likely to undergo mastectomy and/or axillary lymph node dissection. Of patients undergoing upfront surgery, the > 25 months and combined groups were more likely to receive adjuvant chemotherapy, while the never-screened and combined groups were more likely to have nodal disease.

CONCLUSION

Our findings support the initiation of screening mammography at age 40 years to reduce the risk of aggressive treatments for newly diagnosed breast cancers in this group.

Genomic Assays in Node Positive Breast Cancer Patients: A Review

In recent years, developments in breast cancer have allowed yet another realization of individualized medicine in the field of oncology. One of these advances is genomic assays, which are considered elements of standard clinical practice in the management of breast cancer. These assays are widely used today not only to measure recurrence risk in breast cancer patients at an early stage but also to tailor treatment as well and minimize avoidable treatment side effects. At present, genomic tests are applied extensively in node negative disease. In this article, we review the use of these tests in node positive disease, explore their ramifications on neoadjuvant chemotherapy decisions, highlight sufficiently powered recent studies emphasizing their use and review the most recent guidelines.

A Rare Case of Coexisting Breast Cancer and Refractory Acute Myeloid Leukemia

The occurrence of acute myeloid leukemia (AML) within six months from a diagnosis of breast cancer (BC) is rarely reported in the literature, and it is associated with a poor prognosis. We report herein the case of a 40-year-old woman referred to our centre affected by BC and simultaneous AML. The patient proved refractory to first line therapy and achieved complete remission (CR) with a clofarabine-based regimen followed by allogeneic stem cell transplantation (ASCT). Both during salvage chemotherapy and after ASCT, the patient presented severe infectious complications ( acute cholecistytis and Nocardia pneumonia, respectively) treated with surgery, and currently she is alive in CR for both diseases after 29 months of follow-up. The case highlights the importance of a diagnostic assessment of any unexplained cytopenia in association with solid neoplasia under treatment, underlining the feasibility and priority of a timely treatment of the haematological neoplasm in order to achieve long-term survival.

Genetic and Genomic Landscape of Secondary and Therapy-Related Acute Myeloid Leukemia

A subset of acute myeloid leukemia (AML) arises either from an antecedent myeloid malignancy (secondary AML, sAML) or as a complication of DNA-damaging therapy for other cancers (therapy-related myeloid neoplasm, t-MN). These secondary leukemias have unique biological and clinical features that distinguish them from de novo AML. Over the last decade, molecular techniques have unraveled the complex subclonal architecture of sAML and t-MN. In this review, we compare and contrast biological and clinical features of de novo AML with sAML and t-MN. We discuss the role of genetic mutations, including those involved in RNA splicing, epigenetic modification, tumor suppression, transcription regulation, and cell signaling, in the pathogenesis of secondary leukemia. We also discuss clonal hematopoiesis in otherwise healthy individuals, as well as in the context of another malignancy, and how it challenges the conventional notion of sAML/t-MN. We conclude by summarizing the current and emerging treatment strategies, including allogenic transplant, in these complex scenarios.

Clonal hematopoiesis in cancer

Clonal hematopoiesis is a common premalignant condition defined by the abnormal expansion of clonally derived hematopoietic stem cells carrying somatic mutations in leukemia-associated genes. Apart from increasing age, this phenomenon occurs with higher frequency in individuals with lymphoid or solid tumors and is associated with exposures to genotoxic stress. Clonal hematopoiesis in this context confers a greater risk for developing therapy-related myeloid neoplasms and appears to contribute to adverse cancer-related survival through a variety of potential mechanisms. These include alterations of the bone marrow microenvironment, inflammatory changes in clonal effector cells and modulation of immune responses. Understanding how clonal hematopoiesis drives therapy-related myeloid neoplasm initiation and interactions with non-myeloid malignancies will inform screening and surveillance approaches and suggest targeted therapies in this vulnerable population. Here, we examine the clinical implications of clonal hematopoiesis in the cancer setting and discuss potential strategies to mitigate the adverse consequences of clonal expansion.

Discrimination of different cancer types clustering Raman spectra by a super paramagnetic stochastic network approach

Based in high sensitivity and specificity reported recently in detection of the cancer, the technique of Raman spectroscopy is proposed to discriminate between breast cancer, leukemia and cervical cancer using blood serum samples from patients officially diagnosed. In order to classify Raman spectra, clustering method known as Super Paramagnetic Clustering based on statistical physics concepts with a stochastic approach was implemented. Comparing firstly average Raman spectra of the three cancers, some peaks that allowed differentiating one cancer from other were identified, however, other peaks allowed concluding that there are biochemical similarities among them. According to these spectra, the band associated with amide I (1654 cm-1) and one of two shoulders assigned to amide III (1230-1282 cm-1) allowed discriminating leukemia from breast and cervical cancer, whereas band 714 cm-1 (polysaccharides) achieves to differentiate cervical cancer from leukemia and breast cancer, and bulged region, 1040 - 1100 cm-1 (phenylalanine, phospholipid) discriminated breast cancer from leukemia and cervical cancer. Subsequently, Super Paramagnetic Clustering method was applied to Raman spectra to study similarity relationships between cancers based on the biochemical composition of serum samples. Finally, as a cross check method, the standard method to classify Raman spectra of breast cancer, leukemia and cervical cancer, known as principal components analysis, was used showing excellent agreement with results of Super Paramagnetic Clustering method. Preliminary results demonstrated that Raman spectroscopy and Super Paramagnetic Clustering method can be used to discriminate between breast cancer, leukemia and cervical cancer samples using blood serum samples.

Myeloid malignancies after treatment for solid tumours

The cure rate for several solid tumour malignancies including breast cancers, head and neck cancers, bone cancers, and sarcoma has improved remarkably with the advent of neoadjuvant and adjuvant therapies. Unfortunately, exposure to chemotherapy or radiation as a part of these treatments exposes patients to the risk of subsequent myeloid malignancies. Therapy related myeloid malignancies have certain characteristic findings. They typically arise within 10 years of treatment exposure, they are seen in younger patients, and the greatest risk is in patients who receive therapy with alkylating agents or topoisomerase II inhibitors. Solid tumours whose therapies utilize these agents at higher doses, namely bone/soft tissue cancers, testicular cancer, anal cancer, and brain tumours, appear to be the groups at highest risk for T-MN. Beyond these patients, emerging populations diagnosed with T-MN include prior platinum exposure, and patients requiring G-CSF support with chemotherapy.

The leukemia strikes back: a review of pathogenesis and treatment of secondary AML

Secondary AML is associated with a disproportionately poor prognosis, consistently shown to exhibit inferior response rates, event-free survival, and overall survival in comparison with de novo AML. Secondary AML may arise from the evolution of an antecedent hematologic disorder, or it may arise as a complication of prior cytotoxic chemotherapy or radiation therapy in the case of therapy-related AML. Because of the high frequency of poor-risk cytogenetics and high-risk molecular features, such as alterations in TP53, leukemic clones are often inherently chemoresistant. Standard of care induction had long remained conventional 7 + 3 until its reformulation as CPX-351, recently FDA approved specifically for secondary AML. However, recent data also suggests relatively favorable outcomes with regimens based on high-dose cytarabine or hypomethylating agents. With several investigational agents being studied, the therapeutic landscape becomes even more complex, and the treatment approach involves patient-specific, disease-specific, and therapy-specific considerations.

Pathway-based discovery of genetic interactions in breast cancer

Breast cancer is the second largest cause of cancer death among U.S. women and the leading cause of cancer death among women worldwide. Genome-wide association studies (GWAS) have identified several genetic variants associated with susceptibility to breast cancer, but these still explain less than half of the estimated genetic contribution to the disease. Combinations of variants (i.e. genetic interactions) may play an important role in breast cancer susceptibility. However, due to a lack of statistical power, the current tests for genetic interactions from GWAS data mainly leverage prior knowledge to focus on small sets of genes or SNPs that are known to have an association with breast cancer. Thus, many genetic interactions, particularly among novel variants, remain understudied. Reverse-genetic interaction screens in model organisms have shown that genetic interactions frequently cluster into highly structured motifs, where members of the same pathway share similar patterns of genetic interactions. Based on this key observation, we recently developed a method called BridGE to search for such structured motifs in genetic networks derived from GWAS studies and identify pathway-level genetic interactions in human populations. We applied BridGE to six independent breast cancer cohorts and identified significant pathway-level interactions in five cohorts. Joint analysis across all five cohorts revealed a high confidence consensus set of genetic interactions with support in multiple cohorts. The discovered interactions implicated the glutathione conjugation, vitamin D receptor, purine metabolism, mitotic prometaphase, and steroid hormone biosynthesis pathways as major modifiers of breast cancer risk. Notably, while many of the pathways identified by BridGE show clear relevance to breast cancer, variants in these pathways had not been previously discovered by traditional single variant association tests, or single pathway enrichment analysis that does not consider SNP-SNP interactions.

The Role of Carboplatin in the Neoadjuvant Chemotherapy Treatment of Triple Negative Breast Cancer

Triple negative breast (TNBC) cancer constitutes a heterogeneous group of disease with histologic and molecular differences. Complete pathologic response to neoadjuvant chemotherapy (NACT) in TNBC is associated with improved outcomes. Efforts have been made in identifying drug combinations that will increase the response rate to preoperative chemotherapy. In this review we present recent studies that have incorporated carboplatin (Cb) in the NACT of TNBC. We discuss the homologous recombination deficiency score and the somatic or germline mutation for BRCA as potential biomarkers for future selection of patients that could benefit from the addition of Cb to NACT.

Tethered Cord Syndrome-A Study of the Short-Term Effects of Surgical Detethering on Markers of Neuronal Injury and Electrophysiologic Parameters

OBJECTIVE

Several studies have assessed clinical and radiologic outcomes after detethering of the cord for tethered cord syndrome (TCS). However, no data regarding the impact of detethering on the metabolism or electrophysiologic functioning of the cord are available. The aim of this study was to assess the changes in the cerebrospinal fluid (CSF) levels of markers of neuronal injury and alterations in the electrophysiologic functioning of the spinal cord after detethering.

METHODS

This prospective study included patients with congenital TCS. Patients underwent clinical assessment, magnetic resonance imaging, somatosensory evoked potentials (SSEP) study, and CSF biochemical analysis (to estimate lactate, glial fibrillary acidic protein, and S100B levels), before and 3 months after surgery. Clinical and radiologic outcomes were assessed. We studied changes in biochemical and electrophysiologic parameters before and after detethering as surrogate markers for the effects of this intervention.

RESULTS

Twenty-one patients were recruited over 2 years. Detethering led to clinical improvement in 75% of patients with motor deficits, 60% of patients with bladder symptoms, and 50% of patients with gait problems. At 3 months follow-up, 43% (median) of the preoperative vertical tethering was found to be corrected. There was significant reduction in CSF lactate, glial fibrillary acidic protein, and S100B levels as well as a significant decrease in the latencies of the SSEP waves 3 months after surgery.

CONCLUSIONS

Surgical detethering led to a reduction in the CSF levels of the markers of anaerobic metabolism and neuronal injury. There was also a reduction in the latencies of the SSEP waves, indicating better electrophysiologic functioning of the cord.

Somatic mutations in leukocytes infiltrating primary breast cancers

Background:

Malignant transformation requires the interaction of cancer cells with their microenvironment, including infiltrating leukocytes. However, somatic mutational studies have focused on alterations in cancer cells, assuming that the microenvironment is genetically normal. Because we hypothesized that this might not be a valid assumption, we performed exome sequencing and targeted sequencing to investigate for the presence of pathogenic mutations in tumor-associated leukocytes in breast cancers.

Methods:

We used targeted sequencing and exome sequencing to evaluate the presence of mutations in sorted tumor-infiltrating CD45-positive cells from primary untreated breast cancers. We used high-depth sequencing to determine the presence/absence of the mutations we identified in breast cancer-infiltrating leukocytes in purified tumor cells and in circulating blood cells.

Results:

Capture-based sequencing of 15 paired tumor-infiltrating leukocytes and matched germline DNA identified variants in known cancer genes in all 15 primary breast cancer patients in our cohort. We validated the presence of mutations identified by targeted sequencing in infiltrating leukocytes through orthogonal exome sequencing. Ten patients harbored alterations previously reported as somatically acquired variants, including in known leukemia genes (DNTM3A, TET2, and BCOR). One of the mutations observed in the tumor-infiltrating leukocytes was also detected in the circulating leukocytes of the same patients at a lower allele frequency than observed in the tumor-infiltrating cells.

Conclusions:

Here we show that somatic mutations, including mutations in known cancer genes, are present in the leukocytes infiltrating a subset of primary breast cancers. This observation allows for the possibility that the cancer cells interact with mutant infiltrating leukocytes, which has many potential clinical implications.

Appearance of Acute Myelogenous Leukemia (AML) in a Patient with Breast Cancer after Adjuvant Chemotherapy: Case Report and Review of the Literature

Acute Myelogenous Leukemia (AML) is an aggressive hematologic malignancy that cause by abnormal proliferation and accumulation of hematopoietic progenitor cells. A 37-year-old woman referred to oncologic clinic with a self-detected mass and pain in her left breast. The stage of tumor was ΙΙΙA. She was treated with the combination of anthracycline and cyclophosphamide for four courses, followed by four courses of paclitaxel with trastuzumab for one year. After 18 months of the first treatment for breast cancer, her bone marrow biopsy was compatible with AML-M2. Here, we are reporting a young woman case with breast cancer that developed AML malignancy during short interval of therapy.

Epigenetics advancing personalized nanomedicine in cancer therapy

Personalized medicine aims to deliver the right drug to a right patient at the right time. It offers unique opportunities to integrate new technologies and concepts to disease prognosis, diagnosis and therapeutics. While selective personalized therapies are conceptually impressive, the majority of cancer therapies have dismal outcome. Such therapeutic failure could result from no response, drug resistance, disease relapse or severe side effect from improper drug delivery. Nanomedicine, the application of nanotechnology in medicine, has a potential to advance the identification of diagnostic and prognostic biomarkers and the delivery of right drug to disease sites. Epigenetic aberrations dynamically contribute to cancer pathogenesis. Given the individualized traits of epigenetic biomarkers, epigenetic considerations would significantly refine personalized nanomedicine. This review aims to dissect the interface of personalized medicine with nanomedicine and epigenetics. I will outline the progress and highlight challenges and areas that can be further explored perfecting the personalized health care.