A Comprehensive Review of Bioinformatics Tools for Genomic Biomarker Discovery Driving Precision Oncology.

The rapid advancement of high-throughput technologies, particularly next-generation sequencing (NGS), has revolutionized cancer research by enabling the investigation of genetic variations such as SNPs, copy number variations, gene expression, and protein levels. These technologies have elevated the significance of precision oncology, creating a demand for biomarker identification and validation. This review explores the complex interplay of oncology, cancer biology, and bioinformatics tools, highlighting the challenges in statistical learning, experimental validation, data processing, and quality control that underpin this transformative field.

Transcriptome Analysis Identifies Tumor Immune Microenvironment Signaling Networks Supporting Metastatic Castration-Resistant Prostate Cancer.

Prostate cancer (PCa) is the second most common cause of cancer death in American men. Metastatic castration-resistant prostate cancer (mCRPC) is the most lethal form of PCa and preferentially metastasizes to the bones through incompletely understood molecular mechanisms. Herein, we processed RNA sequencing data from patients with mCRPC ( = 60) and identified 14 gene clusters (modules) highly correlated with mCRPC bone metastasis.

A Scoping Review of Professionalism in Neurosurgery.

Background And Objectives: The Accreditation Council for Graduate Medical Education's Milestones provides a foundation for professionalism in residency training. Specific professionalism concepts from neurosurgery could augment and expand milestones for the specialty. We reviewed the current literature and identified professionalism concepts within the context of neurosurgical practice and training.

Complications and Avoidance in Adult Spinal Deformity Surgery.

Adult spinal deformity (ASD) is a complex disease that can result in significant disability. Although surgical treatment has been shown to be of benefit, the complication rate in the perioperative and postoperative periods can be as high as 70%. Some of the most common complications of ASD surgery include intraoperative cerebrospinal fluid leak, high blood loss, new neurologic deficit, hardware failure, proximal junctional kyphosis/failure, pseudarthrosis, surgical site infection, and medical complications.

Increasing Clinical Trial Participation of Black Women Diagnosed with Breast Cancer.

Despite racial disparities in breast cancer mortality, Black women remain underrepresented in clinical trials. In this mixed methods research, 48 Black women were engaged via focus group discussions and in-depth interviews to better understand the lived experience of women with breast cancer. The results of this qualitative study informed the development of a subsequent online survey to identify barriers, motivators, and other factors that influence decision-making by Black women diagnosed with breast cancer when considering clinical trial participation.

Alternatives to DEXA for the assessment of bone density: a systematic review of the literature and future recommendations.

Objective: Osteoporosis has significant implications in spine fusion surgery, for which reduced spinal bone mineral density (BMD) can result in complications and poorer outcomes. Currently, dual-energy x-ray absorptiometry (DEXA) is the gold standard for radiographic diagnosis of osteoporosis, although DEXA accuracy may be limited by the presence of degenerative spinal pathology. In recent years, there has been an evolving interest in using alternative imaging, including CT and MRI, to assess BMD.

Racial disparities in Black men with prostate cancer: A literature review.

Black men are disproportionately affected by prostate cancer (PCa), with earlier presentation, more aggressive disease, and higher mortality rates versus White men. Furthermore, Black men have less access to PCa treatment and experience longer delays between diagnosis and treatment. In this review, the authors discuss the factors contributing to racial disparities and present solutions to improve access to care and increase clinical trial participation among Black men with PCa.

Multivariant Transcriptome Analysis Identifies Modules and Hub Genes Associated with Poor Outcomes in Newly Diagnosed Multiple Myeloma Patients.

The molecular mechanisms underlying chemoresistance in some newly diagnosed multiple myeloma (MM) patients receiving standard therapies (lenalidomide, bortezomib, and dexamethasone) are poorly understood. Identifying clinically relevant gene networks associated with death due to MM may uncover novel mechanisms, drug targets, and prognostic biomarkers to improve the treatment of the disease. This study used data from the MMRF CoMMpass RNA-seq dataset (N = 270) for weighted gene co-expression network analysis (WGCNA), which identified 21 modules of co-expressed genes.

Proteomic profiling based classification of CLL provides prognostication for modern therapy and identifies novel therapeutic targets.

Protein expression for 384 total and post-translationally modified proteins was assessed in 871 CLL and MSBL patients and was integrated with clinical data to identify strategies for improving diagnostics and therapy, making this the largest CLL proteomics study to date. Proteomics identified six recurrent signatures that were highly prognostic of survival and time to first or second treatment at three levels: individual proteins, when grouped into 40 functionally related groups (PFGs), and systemically in signatures (SGs). A novel SG characterized by hairy cell leukemia like proteomics but poor therapy response was discovered.

Identification of Gene Co-Expression Networks Associated with Consensus Molecular Subtype-1 of Colorectal Cancer.

Colorectal cancer (CRC) is driven in part by dysregulated Wnt, Ras-Raf-MAPK, TGF-β, and PI3K-Akt signaling. The progression of CRC is also promoted by molecular alterations and heterogeneous-yet interconnected-gene mutations, chromosomal instability, transcriptomic subtypes, and immune signatures. Genomic alterations of CRC progression lead to changes in RNA expression, which support CRC metastasis.

RPPA-based proteomics recognizes distinct epigenetic signatures in chronic lymphocytic leukemia with clinical consequences.

The chronic lymphocytic leukemia (CLL) armamentarium has evolved significantly, with novel therapies that inhibit Bruton Tyrosine Kinase, PI3K delta and/or the BCL2 protein improving outcomes. Still, the clinical course of CLL patients is highly variable and most previously recognized prognostic features lack the capacity to predict response to modern treatments indicating the need for new prognostic markers. In this study, we identified four epigenetically distinct proteomic signatures of a large cohort of CLL and related diseases derived samples (n = 871) using reverse phase protein array technology.

Multivariate transcriptome analysis identifies networks and key drivers of chronic lymphocytic leukemia relapse risk and patient survival.

Background: Chronic lymphocytic leukemia (CLL) is an indolent heme malignancy characterized by the accumulation of CD5 CD19 B cells and episodes of relapse. The biological signaling that influence episodes of relapse in CLL are not fully described. Here, we identify gene networks associated with CLL relapse and survival risk.

A network approach reveals driver genes associated with survival of patients with triple-negative breast cancer.

We aimed to identify triple-negative breast cancer (TNBC) drivers that regulate survival time as predictive signatures that improve TNBC prognostication. Breast cancer (BrCa) transcriptomic tumor biopsies were analyzed, identifying network communities enriched with TNBC-specific differentially expressed genes (DEGs) and correlated strongly to TNBC status. Two anticorrelated modules correlated strongly to TNBC subtype and survival.

Selective Targeting of the Hedgehog Signaling Pathway by PBM Nanoparticles in Docetaxel-Resistant Prostate Cancer.

An abnormality in hedgehog (Hh) signaling has been implicated in the progression of prostate cancer (PCa) to a more aggressive and therapy-resistant disease. Our assessments of human PCa tissues have shown an overexpression of the Hh pathway molecules, glioma-associated oncogene homolog 1 (GLI-1), and sonic hedgehog (SHH). The effect of the natural compound thymoquinone (TQ) in controlling the expression of Hh signaling molecules in PCa was investigated in this study.

Dissecting the Financial Relationship Between Industry and Academic Neurosurgery.

Background: Established by the Centers for Medicare and Medicaid Services (CMS), the Open Payments Database (OPD) has reported industry payments to physicians since August 2013.

Objective: To evaluate the frequency, type, and value of payments received by academic neurosurgeons in the United States over a 5-yr period (2014-2018).

Methods: The OPD was queried for attending neurosurgeons from all neurosurgical training programs in the United States (n = 116).

Predicting Surgical Intervention in Cerebellar Stroke: A Quantitative Retrospective Analysis.

Background: Debate still exists regarding whether preventive surgical decompression should be offered to high-risk patients experiencing cerebellar stroke. This study aimed to predict neurologic decline based on risk factors, volumetric analysis, and imaging characteristics.

Methods: This retrospective cohort study comprised patients ≥18 years who presented with acute cerebellar ischemic stroke (CIS) between January 2011 and December 2016.

Role of natural compounds in preventing and treating breast cancer.

Breast cancer (BrCa) is the most commonly diagnosed cancer and the second leading cause of cancer-related death in women. Alarming increases in the cases quests for more effective treatment of BrCa. As most chemotherapeutic drugs are associated with drug resistance, cancer relapse, and side effects, scientists are turning to agents with more efficacy, such as natural compounds for treatment and prevention of BrCa.

Innovation, Royalties, and Introduction of the Patent Hirsch Index within U.S. Academic Neurosurgery.

Background: Historically, practicing neurosurgeons have been key drivers of neurosurgical innovation. We sought to describe the patents held by U.S.

Transcriptome Network Analysis Identifies CXCL13-CXCR5 Signaling Modules in the Prostate Tumor Immune Microenvironment.

The tumor immune microenvironment (TIME) consists of multiple cell types that contribute to the heterogeneity and complexity of prostate cancer (PCa). In this study, we sought to understand the gene-expression signature of patients with primary prostate tumors by investigating the co-expression profiles of patient samples and their corresponding clinical outcomes, in particular "disease-free months" and "disease reoccurrence". We tested the hypothesis that the CXCL13-CXCR5 axis is co-expressed with factors supporting TIME and PCa progression.

Shunt Failure-The First 30 Days.

Background: Incontrovertible predictors of shunt malfunction remain elusive.

Objective: To determine predictors of shunt failure within 30 d of index surgery.

Methods: This was a single-center retrospective cohort study from January 2010 through November 2016.

SMR peptide antagonizes mortalin promoted release of extracellular vesicles and affects mortalin protection from complement-dependent cytotoxicity in breast cancer cells and leukemia cells.

Mortalin/GRP-75/mt-hsp70 is a mitochondrial chaperone protein, found in the cytoplasm, endoplasmic reticulum and cytoplasmic vesicles. It functions in many cellular processes such as mitochondrial biogenesis, intracellular trafficking, cell proliferation, signaling, immortalization and tumorigenesis. Thus, inhibition of mortalin is a promising avenue for cancer therapy.