Solving the :: Fusion Nomenclature Challenge for File and Directory Naming.

Following recommendations from various consortia and professional societies, the double-colon symbol (::) has become an integral part of gene fusion nomenclature (e.g., EML4::ALK).

RNA sequencing and immunohistochemistry jointly improve tumor biomarker interpretation.

This study aimed to assess the correlation between RNA sequencing (RNA-seq) and immunohistochemistry (IHC) in detecting key cancer biomarkers across solid tumors, and then, to establish RNA-seq thresholds that accurately reflect clinical IHC classifications. Expression levels of nine biomarkers-ESR1, PGR, AR, MKI67, ERBB2, CD274, CDX2, KRT7, and KRT20-were analyzed in 365 formalin-fixed, paraffin-embedded samples from breast, lung, gastrointestinal, and other solid carcinomas. Correlations between RNA-seq data and IHC scores were determined using Spearman's correlation coefficients, with RNA-seq cut-offs established to distinguish positive from negative IHC scores.

Enhancing diagnostic innovation by leveraging the co-creation approach.

Digital innovation in precision diagnostics requires addressing complex challenges, such as implementation, adoption, equity, and sustainability. This study introduces a co-creation framework that leverages the pre-competitive space to drive collaborative innovation in personalized diagnostics. Over 5 years, a multidisciplinary community of stakeholders from computational pathology, oncology, genetics, digital medicine, and industry engaged in design-thinking workshops to identify unmet medical needs and co-develop solutions.

Immune Composition and Immunotherapy Outcomes of Mesothelioma With BAP1, CDKN2A, MTAP, and NF2 Alterations.

Introduction: First-line mesothelioma treatment paradigms prioritize histology without integrating molecular features. Findings from other thoracic cancers suggest that tumor immune microenvironment (TME) composition and immunotherapy efficacy are informed by genomic profile. Mesothelioma studies exploring the relationship between molecular alterations, immune infiltrate, and immunotherapy outcomes are needed.

Morphological Bone Score as a Predictive Tool for Molecular Profiling Success.

Decalcification of bone-containing tumor samples serves to soften tissues before histologic processing. However, it can lead to nucleic acid degradation, resulting in next-generation sequencing failures that impede diagnostic solutions for patients. The Morphological Bone Score (MBS) described herein optimizes the assessment of decalcified tissue samples, consequently improving both diagnostic accuracy and cost efficiency in molecular genetic laboratories.

The Breast Cancer Classifier refines molecular breast cancer classification to delineate the HER2-low subtype.

Current breast cancer classification methods, particularly immunohistochemistry and PAM50, face challenges in accurately characterizing the HER2-low subtype, a therapeutically relevant entity with distinct biological features. This notable gap can lead to misclassification, resulting in inappropriate treatment decisions and suboptimal patient outcomes. Leveraging RNA-seq and machine-learning algorithms, we developed the Breast Cancer Classifier (BCC), a unique transcriptomic classifier for more precise breast cancer subtyping, specifically by delineating and incorporating HER2-low as a distinct subtype.

Tumor-immune partitioning and clustering algorithm for identifying tumor-immune cell spatial interaction signatures within the tumor microenvironment.

Background: Growing evidence supports the importance of characterizing the organizational patterns of various cellular constituents in the tumor microenvironment in precision oncology. Most existing data on immune cell infiltrates in tumors, which are based on immune cell counts or nearest neighbor-type analyses, have failed to fully capture the cellular organization and heterogeneity.

Methods: We introduce a computational algorithm, termed Tumor-Immune Partitioning and Clustering (TIPC), that jointly measures immune cell partitioning between tumor epithelial and stromal areas and immune cell clustering versus dispersion.

Quantifying cell divisions along evolutionary lineages in cancer.

Cell division drives somatic evolution but is challenging to quantify. We developed a framework to count cell divisions with DNA replication-related mutations in polyguanine homopolymers. Analyzing 505 samples from 37 patients, we studied the milestones of colorectal cancer evolution.

Ultrasensitive detection of intact SARS-CoV-2 particles in complex biofluids using microfluidic affinity capture.

Measuring virus in biofluids is complicated by confounding biomolecules coisolated with viral nucleic acids. To address this, we developed an affinity-based microfluidic device for specific capture of intact severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Our approach used an engineered angiotensin-converting enzyme 2 to capture intact virus from plasma and other complex biofluids.

Determining the time to cholangiocarcinoma in pediatric-onset PSC-IBD.

Primary sclerosing cholangitis (PSC) is a risk factor for cholangiocarcinoma. When a child is diagnosed with both PSC and inflammatory bowel disease (IBD), evidence-based information on counseling families and risk management of developing cholangiocarcinoma is limited. In this case series (PubMed/collaborators), we included patients with PSC-IBD who developed cholangiocarcinoma and contacted authors to determine an event curve specifying the time between the second diagnosis (IBD or PSC) and a diagnosis of cholangiocarcinoma.

Comparative Analysis of MYB Expression by Immunohistochemistry and RNA Sequencing in Clinical Gene Fusion Detection in Adenoid Cystic Carcinoma.

Purpose: MYB has been shown to play a central role in oncogenesis in a majority of adenoid cystic carcinomas (ACC). Testing for MYB expression via immunohistochemistry (IHC) or testing for the MYB gene fusion by next-generation sequencing (NGS) have become useful tools for the diagnosis of ACC. In addition, detection of MYB expression may have implications for patient management.

Developmental mosaicism underlying EGFR-mutant lung cancer presenting with multiple primary tumors.

Although the development of multiple primary tumors in smokers with lung cancer can be attributed to carcinogen-induced field cancerization, the occurrence of multiple tumors at presentation in individuals with EGFR-mutant lung cancer who lack known environmental exposures remains unexplained. In the present study, we identified ten patients with early stage, resectable, non-small cell lung cancer who presented with multiple, anatomically distinct, EGFR-mutant tumors. We analyzed the phylogenetic relationships among multiple tumors from each patient using whole-exome sequencing (WES) and hypermutable poly(guanine) (poly(G)) repeat genotyping as orthogonal methods for lineage tracing.

Clinical outcomes and ctDNA correlates for CAPOX BETR: a phase II trial of capecitabine, oxaliplatin, bevacizumab, trastuzumab in previously untreated advanced HER2+ gastroesophageal adenocarcinoma.

Preclinical studies suggest that simultaneous HER2/VEGF blockade may have cooperative effects in gastroesophageal adenocarcinomas. In a single-arm investigator initiated clinical trial for patients with untreated advanced HER2+ gastroesophageal adenocarcinoma, bevacizumab was added to standard of care capecitabine, oxaliplatin, and trastuzumab in 36 patients (NCT01191697). Primary endpoint was objective response rate and secondary endpoints included safety, duration of response, progression free survival, and overall survival.

Technology and Future of Multi-Cancer Early Detection.

Cancer remains a significant global health challenge due to its high morbidity and mortality rates. Early detection is essential for improving patient outcomes, yet current diagnostic methods lack the sensitivity and specificity needed for identifying early-stage cancers. Here, we explore the potential of multi-omics approaches, which integrate genomic, transcriptomic, proteomic, and metabolomic data, to enhance early cancer detection.

Harmonized cross-species cell atlases of trigeminal and dorsal root ganglia.

Sensory neurons in the dorsal root ganglion (DRG) and trigeminal ganglion (TG) are specialized to detect and transduce diverse environmental stimuli to the central nervous system. Single-cell RNA sequencing has provided insights into the diversity of sensory ganglia cell types in rodents, nonhuman primates, and humans, but it remains difficult to compare cell types across studies and species. We thus constructed harmonized atlases of the DRG and TG that describe and facilitate comparison of 18 neuronal and 11 non-neuronal cell types across six species and 31 datasets.

Bridging the Clinical-Computational Transparency Gap in Digital Pathology.

Context.—: Computational pathology combines clinical pathology with computational analysis, aiming to enhance diagnostic capabilities and improve clinical productivity. However, communication barriers between pathologists and developers often hinder the full realization of this potential.

Rapid tumor DNA analysis of cerebrospinal fluid accelerates treatment of central nervous system lymphoma.

Delays and risks associated with neurosurgical biopsies preclude timely diagnosis and treatment of central nervous system (CNS) lymphoma and other CNS neoplasms. We prospectively integrated targeted rapid genotyping of cerebrospinal fluid (CSF) into the evaluation of 70 patients with CNS lesions of unknown cause. Participants underwent genotyping of CSF-derived DNA using a quantitative polymerase chain reaction-based approach for parallel detection of single-nucleotide variants in the MYD88, TERT promoter, IDH1, IDH2, BRAF, and H3F3A genes within 80 minutes of sample acquisition.

Virus-Induced Acute Respiratory Distress Syndrome Causes Cardiomyopathy Through Eliciting Inflammatory Responses in the Heart.

Background: Viral infections can cause acute respiratory distress syndrome (ARDS), systemic inflammation, and secondary cardiovascular complications. Lung macrophage subsets change during ARDS, but the role of heart macrophages in cardiac injury during viral ARDS remains unknown. Here we investigate how immune signals typical for viral ARDS affect cardiac macrophage subsets, cardiovascular health, and systemic inflammation.