Predicting patient outcomes after treatment with immune checkpoint blockade: A review of biomarkers derived from diverse data modalities

Immune checkpoint blockade (ICB) therapy targeting cytotoxic T-lymphocyte-associated protein 4, programmed death 1, and programmed death ligand 1 has shown durable remission and clinical success across different cancer types. However, patient outcomes vary among disease indications. Studies have identified prognostic biomarkers associated with immunotherapy response and patient outcomes derived from diverse data types, including next-generation bulk and single-cell DNA, RNA, T cell and B cell receptor sequencing data, liquid biopsies, and clinical imaging. Owing to inter- and intra-tumor heterogeneity and the immune system's complexity, these biomarkers have diverse efficacy in clinical trials of ICB. Here, we review the genetic and genomic signatures and image features of ICB studies for pan-cancer applications and specific indications. We discuss the advantages and disadvantages of computational approaches for predicting immunotherapy effectiveness and patient outcomes. We also elucidate the challenges of immunotherapy prognostication and the discovery of novel immunotherapy targets.

Peripheral blood TCR clonotype diversity as an age-associated marker of breast cancer progression

Immune escape is a prerequisite for tumor growth. We previously described a decline in intratumor activated cytotoxic T cells and T cell receptor (TCR) clonotype diversity in invasive breast carcinomas compared to ductal carcinoma in situ (DCIS), implying a central role of decreasing T cell responses in tumor progression. To determine potential associations between peripheral immunity and breast tumor progression, here, we assessed the peripheral blood TCR clonotype of 485 breast cancer patients diagnosed with either DCIS or de novo stage IV disease at younger (<45) or older (≥45) age. TCR clonotype diversity was significantly lower in older compared to younger breast cancer patients regardless of tumor stage at diagnosis. In the younger age group, TCR-α clonotype diversity was lower in patients diagnosed with de novo stage IV breast cancer compared to those diagnosed with DCIS. In the older age group, DCIS patients with higher TCR-α clonotype diversity were more likely to have a recurrence compared to those with lower diversity. Whole blood transcriptome profiles were distinct depending on the TCR-α Chao1 diversity score. There were more CD8+ T cells and a more active immune environment in DCIS tumors of young patients with higher peripheral blood TCR-α Chao1 diversity than in those with lower diversity. These results provide insights into the role that host immunity plays in breast cancer development across different age groups.

Tutorial: integrative computational analysis of bulk RNA-sequencing data to characterize tumor immunity using RIMA

RNA-sequencing (RNA-seq) has become an increasingly cost-effective technique for molecular profiling and immune characterization of tumors. In the past decade, many computational tools have been developed to characterize tumor immunity from gene expression data. However, the analysis of large-scale RNA-seq data requires bioinformatics proficiency, large computational resources and cancer genomics and immunology knowledge. In this tutorial, we provide an overview of computational analysis of bulk RNA-seq data for immune characterization of tumors and introduce commonly used computational tools with relevance to cancer immunology and immunotherapy. These tools have diverse functions such as evaluation of expression signatures, estimation of immune infiltration, inference of the immune repertoire, prediction of immunotherapy response, neoantigen detection and microbiome quantification. We describe the RNA-seq IMmune Analysis (RIMA) pipeline integrating many of these tools to streamline RNA-seq analysis. We also developed a comprehensive and user-friendly guide in the form of a GitBook with text and video demos to assist users in analyzing bulk RNA-seq data for immune characterization at both individual sample and cohort levels by using RIMA.

A Foley catheter 'the jack of all trades': a literature review of its common and novel uses

The Foley catheter is one of the most commonly used devices in modern surgical practice. Developed for draining the urinary bladder, this humble catheter has been employed for many other purposes ranging from urine output monitoring to complex urological investigations. Over time, it has evolved into being applied in more complex and innovative ways in various other specialties apart from urology. In this review article, we describe some of the common and novel uses of this deceptively simple device, and discuss the scope of its application in modern medicine.

333 A Rare Case of Skeletal Muscle Metastasis of Colorectal Cancer

Introduction

Colorectal carcinoma is one of the most commonly diagnosed cancers. Metastasis is seen in the liver, lung, peritonium and bone. Though skeletal muscles make up a majority of our body mass, they are an extremely rare site for metastasis

A 74 y/male known to have total ulcerative colitis was put on the 2WW due to change in bowel habits, weight loss and anemia. Investigations revealed a large cavitating lesion in the right colon with no evidence of metastasis. He underwent an open total pan procto-colectomy, small bowel resection and end ileostomy

Histopathology showed the tumour was a completely excised adenocarcinoma

During surveillance it was noted his CEA levels were high, for which he had a host of investigations including a CT scan and a PET scan, all of which had no interval changes.

He mentioned that he noticed a lump in his left thigh. Orthopedicians advised an MRI scan which showed a tissue lump covering the front of the thigh, within the vastus medialis.

A biopsy revealed metastatic adenocarcinoma.

He also had left wrist pain. A thorough examination revealed a hard mass within the swelling. Ultrasound confirmed a solid well circumscribed mass with vascularity.

Given the above information the patient felt he would be like to complete the remaining of his life with dignity and comfort at home and was fast-track discharged.

Discussion

Skeletal muscle metastasis of colorectal cancers is always associated with a prognosis that is somber and terminal. A high degree of suspicion is needed for diagnosis.

The initial Trinidad experience with Cine MRI in clinical cardiology

We describe the initial Trinidad experience with Magnetic Resonance Imaging (MRI) and Cine MRI as a diagnostic tool in clinical cardiology. Six patients from the following categories were referred for Cine MRI evaluation: congenital heart disease, valvular heart disease, aortic diseases, cardiomyopathy and intracardiac mass. All patients underwent echocardiography. MRI and Cine MRI were performed on all patients using a Siemens Magnetom 1.0 Tesla MR system at MRI Trinidad and Tobago Ltd. Selected patients underwent Angiography and/or computed tomography (CT) scanning. Clinical data and images of the six patients evaluated are described. MRI and Cine MRI provided excellent anatomical and functional details of the heart and aorta in five patients with dissection of the aorta, aneurysm of the ascending aorta, suspected left ventricular apical thrombus, infiltrative cardiomyopathy and arrhythmogenic right ventricular dysplasia. Technical difficulty was experienced with one patient who had a congenital defect (common atrium). In this study, Cine MRI provided excellent images in all but one patient. This new noninvasive technique enhanced diagnostic capabilities and facilitated management in patients with certain cardiovascular diseases.