SCAN-ACT: adoptive T cell therapy target discovery through single-cell transcriptomics.

Background: The FDA approval of T cell receptor-engineered T cells (TCR-T) for synovial sarcoma demonstrates the potential for adoptive T cell therapies (ACTs) in solid tumors. However, the paucity of tumor-associated targets without expression in normal tissues remains a major bottleneck, especially in rare cancer subtypes.

Methods: We developed a comprehensive computational pipeline called SCAN-ACT that leverages single-cell RNA sequencing and multi-omics data from tumor and normal tissues to nominate and prioritize putative targets for both chimeric antigen receptor (CAR)- and TCR-T cells.

Scalp EEG predicts intracranial brain activity in humans.

Inferring deep brain activity from noninvasive scalp recordings remains a fundamental challenge in neuroscience. Here, we analyzed concurrent scalp and intracranial recordings from 1918 electrode contacts across 20 patients affected by drug-resistant epilepsy undergoing intracranial depth electrode monitoring for pre-surgical evaluation to establish predictive relationships between surface and deep brain signals. Using regularized and cross-validated linear regression within subjects, we demonstrate that scalp recordings can predict spontaneous intracranial activity, with accuracy varying by region, depth, and frequency.

Rapid, Point-of-Care Bone Marrow Aspirate Adequacy Assessment Via Deep Ultraviolet Microscopy.

Bone marrow aspirations are pivotal for diagnosing and monitoring various hematological conditions, including cancers. However, a significant portion (10%-50%) of aspirations yield suboptimal or inadequate diagnostic material. The difficulty and scarcity of bedside adequacy assessment strategies further exacerbate the challenges in this procedure, which can consequently lead to delays in diagnosis and treatment, among other complications.

Evolutionary Pressures Shape Undifferentiated Pleomorphic Sarcoma Development and Radiotherapy Response.

Radiotherapy is an integral component in the treatment of many types of cancer, with approximately half of patients with cancer receiving radiotherapy. Systemic therapy applies pressure that can select for resistant tumor subpopulations, underscoring the importance of understanding how radiation impacts tumor evolution to improve treatment outcomes. We integrated temporal genomic profiling of 120 spatially distinct tumor regions from 20 patients with undifferentiated pleomorphic sarcomas (UPS), longitudinal circulating tumor DNA analysis, and evolutionary biology computational pipelines to study UPS evolution during tumorigenesis and in response to radiotherapy.

Benchmarking the speed-accuracy tradeoff in object recognition by humans and neural networks.

Active object recognition, fundamental to tasks like reading and driving, relies on the ability to make time-sensitive decisions. People exhibit a flexible tradeoff between speed and accuracy, a crucial human skill. However, current computational models struggle to incorporate time.

Enhancing radiotherapy response via intratumoral injection of a TLR9 agonist in autochthonous murine sarcomas.

Radiation therapy (RT) is frequently used to treat cancers, including soft-tissue sarcomas. Prior studies established that the toll-like receptor 9 (TLR9) agonist cytosine-phosphate-guanine oligodeoxynucleotide (CpG) enhances the response to RT in transplanted tumors, but the mechanisms of this enhancement remain unclear. Here, we used CRISPR/Cas9 and the chemical carcinogen 3-methylcholanthrene (MCA) to generate autochthonous soft-tissue sarcomas with high tumor mutation burden.

Spatial phenotyping of nodular lymphocyte predominant Hodgkin lymphoma and T-cell/histiocyte-rich large B-cell lymphoma.

Nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) is a rare lymphoma with sparse tumor B-cells and a favorable prognosis. Variant growth patterns of NLPHL, however, often show advanced stage, progression to T-cell/histiocyte-rich large B-cell lymphoma (THRLBCL) and a worse prognosis. We studied the tumor microenvironment (TME) of NLPHL and THRLBCL using highplex imaging and spatial profiling at the single cell level.

Simultaneous invasive and non-invasive recordings in humans: A novel Rosetta stone for deciphering brain activity.

Simultaneous noninvasive and invasive electrophysiological recordings provide a unique opportunity to achieve a comprehensive understanding of human brain activity, much like a Rosetta stone for human neuroscience. In this review we focus on the increasingly-used powerful combination of intracranial electroencephalography (iEEG) with scalp electroencephalography (EEG) or magnetoencephalography (MEG). We first provide practical insight on how to achieve these technically challenging recordings.

Sarcoma microenvironment cell states and ecosystems are associated with prognosis and predict response to immunotherapy.

Characterization of the diverse malignant and stromal cell states that make up soft tissue sarcomas and their correlation with patient outcomes has proven difficult using fixed clinical specimens. Here, we employed EcoTyper, a machine-learning framework, to identify the fundamental cell states and cellular ecosystems that make up sarcomas on a large scale using bulk transcriptomes with clinical annotations. We identified and validated 23 sarcoma-specific, transcriptionally defined cell states, many of which were highly prognostic of patient outcomes across independent datasets.

Enhancing radiotherapy response via intratumoral injection of the TLR9 agonist CpG to stimulate CD8 T cells in an autochthonous mouse model of sarcoma.

Radiation therapy is frequently used to treat cancers including soft tissue sarcomas. Prior studies established that the toll-like receptor 9 (TLR9) agonist cytosine-phosphate-guanine oligodeoxynucleotide (CpG) enhances the response to radiation therapy (RT) in transplanted tumors, but the mechanism(s) remain unclear. Here, we used CRISPR/Cas9 and the chemical carcinogen 3-methylcholanthrene (MCA) to generate autochthonous soft tissue sarcomas with high tumor mutation burden.

Investigating the tissue specificity and prognostic impact of cis-regulatory cancer risk variants.

The tissue-specific incidence of cancers and their genetic basis are poorly understood. Although prior studies have shown global correlation across tissues for cancer risk single-nucleotide polymorphisms (SNPs) identified through genome-wide association studies (GWAS), any shared functional regulation of gene expression on a per SNP basis has not been well characterized. We set to quantify cis-mediated gene regulation and tissue sharing for SNPs associated with eight common cancers.

Monitoring Sarcoma Response to Immune Checkpoint Inhibition and Local Cryotherapy with Circulating Tumor DNA Analysis.

Purpose: Immune checkpoint inhibition has led to promising responses in soft tissue sarcomas (STS), but the majority of patients do not respond and biomarkers of response will be crucial. Local ablative therapies may augment systemic responses to immunotherapy. We evaluated circulating tumor DNA (ctDNA) as a biomarker of response in patients treated on a trial combining immunotherapy with local cryotherapy for advanced STS.

Aortic valve surgery for native valve endocarditis in extreme obesity.

Surgical aortic valve replacement represents a class one indication in the setting of aortic valve endocarditis and decompensated heart failure secondary to aortic regurgitation as per the European Society of Cardiology. However, extreme obesity, whereby the body mass index (BMI) >40 kg/m, represents a challenging cohort of patients. Performing cardiac surgery in the bariatric population is fraught with challenges pertaining to intraoperative issues of surgical access and approach.

A Century of Fractionated Radiotherapy: How Mathematical Oncology Can Break the Rules.

Radiotherapy is involved in 50% of all cancer treatments and 40% of cancer cures. Most of these treatments are delivered in fractions of equal doses of radiation (Fractional Equivalent Dosing (FED)) in days to weeks. This treatment paradigm has remained unchanged in the past century and does not account for the development of radioresistance during treatment.

Reinforcement learning and its connections with neuroscience and psychology.

Reinforcement learning methods have recently been very successful at performing complex sequential tasks like playing Atari games, Go and Poker. These algorithms have outperformed humans in several tasks by learning from scratch, using only scalar rewards obtained through interaction with their environment. While there certainly has been considerable independent innovation to produce such results, many core ideas in reinforcement learning are inspired by phenomena in animal learning, psychology and neuroscience.

Clinical whole genome sequencing as a first-tier test at a resource-limited dysmorphology clinic in Mexico.

Patients with rare, undiagnosed, or genetic disease (RUGD) often undergo years of serial testing, commonly referred to as the "diagnostic odyssey". Patients in resource-limited areas face even greater challenges-a definitive diagnosis may never be reached due to difficulties in gaining access to clinicians, appropriate specialists, and diagnostic testing. Here, we report on a collaboration of the Illumina iHope Program with the Foundation for the Children of the Californias and Hospital Infantil de Las Californias, to enable deployment of clinical whole genome sequencing (cWGS) as first-tier test in a resource-limited dysmorphology clinic in northern Mexico.

Copy-number variants in clinical genome sequencing: deployment and interpretation for rare and undiagnosed disease.

Purpose: Current diagnostic testing for genetic disorders involves serial use of specialized assays spanning multiple technologies. In principle, genome sequencing (GS) can detect all genomic pathogenic variant types on a single platform. Here we evaluate copy-number variant (CNV) calling as part of a clinically accredited GS test.

Laminated Object Manufacturing of 3D-Printed Laser-Induced Graphene Foams.

Laser-induced graphene (LIG), a graphene structure synthesized by a one-step process through laser treatment of commercial polyimide (PI) film in an ambient atmosphere, has been shown to be a versatile material in applications ranging from energy storage to water treatment. However, the process as developed produces only a 2D product on the PI substrate. Here, a 3D LIG foam printing process is developed on the basis of laminated object manufacturing, a widely used additive-manufacturing technique.

Detection of long repeat expansions from PCR-free whole-genome sequence data.

Identifying large expansions of short tandem repeats (STRs), such as those that cause amyotrophic lateral sclerosis (ALS) and fragile X syndrome, is challenging for short-read whole-genome sequencing (WGS) data. A solution to this problem is an important step toward integrating WGS into precision medicine. We developed a software tool called ExpansionHunter that, using PCR-free WGS short-read data, can genotype repeats at the locus of interest, even if the expanded repeat is larger than the read length.

True Lumen Perfusion Technique for Extensive Aortic Dissections Involving the Neck and Femoral Vessels.

Cannulation and perfusion in extensive aortic dissection involving the neck and femoral vessels is challenging in view of false lumen cannulation and attendant malperfusion syndromes. Although a number of methods have been described, our technique of cannulation and perfusion through right atrial-to-left atrial bypass and innominate artery transection ensures adequate brain perfusion and visceral organ true lumen perfusion during the entire duration of cardiopulmonary bypass. This procedure can be applied to all varieties of extensive type A aortic dissections involving the neck and femoral vessels.

Identification and functional characterization of tRNA-derived RNA fragments (tRFs) in respiratory syncytial virus infection.

The discovery of small noncoding RNAs (sncRNAs) with regulatory functions is a recent breakthrough in biology. Among sncRNAs, microRNA (miRNA), derived from host or virus, has emerged as elements with high importance in control of viral replication and host responses. However, the expression pattern and functional aspects of other types of sncRNAs, following viral infection, are unexplored.

Mutational signatures of de-differentiation in functional non-coding regions of melanoma genomes.

Much emphasis has been placed on the identification, functional characterization, and therapeutic potential of somatic variants in tumor genomes. However, the majority of somatic variants lie outside coding regions and their role in cancer progression remains to be determined. In order to establish a system to test the functional importance of non-coding somatic variants in cancer, we created a low-passage cell culture of a metastatic melanoma tumor sample.