Differential Spatial Gene and Protein Expression Associated with Recurrence Following Chemoradiation for Localized Anal Squamous Cell Cancer

The Transcriptomic Landscapes of Appendiceal Primary and Metastatic Tumors are Distinct

BACKGROUND

Improved understanding about the pathobiology of appendiceal cancers (AC) and resulting metastasis is required for the development of novel treatments. The tumor microenvironment in AC is heterogeneous and incompletely characterized. The objective of this study was to leverage spatial high-plex technology to evaluate the transcriptomic landscape of epithelial and stromal cells in primary AC tumors, adjacent normal appendix, and corresponding peritoneal metastasis.

METHODS

A tissue microarray (TMA) containing cores from 14 unique patients having matched primary tumor, adjacent normal appendix, and peritoneal metastases was analyzed with digital spatial profiling (NanoString, GeoMx) using pancytokeratin (PCK) to delineate stroma (PCK-) from epithelium (PCK+). Then RNA sequencing was performed to measure transcript abundance separately within the stromal and epithelial compartments.

RESULTS

Transcriptomic analysis demonstrated differences between tumor and stromal compartments in both primary tumor and metastatic sites. Primary and metastatic tumor stroma (PCK-) demonstrated greater expression of ribosomal biogenesis pathways than normal appendiceal tissue. Primary and metastatic tumors were generally similar with respect to transcription. However, within the epithelial compartment (PCK+), peritoneal metastases exhibited upregulated cytoskeletal and collagen metabolism pathways/genes compared with primary tumor.

CONCLUSIONS

The study data indicated that although appendiceal peritoneal disease is transcriptionally similar to the primary tumor, potentially important distinctions exist between metastatic and primary disease. Differences appear to be driven predominantly by changes in collagen metabolism at the peritoneal site. A better understanding of both tumor and stromal compartments of metastatic disease will be essential to improving therapeutic options, specifically systemic treatment, which is characteristically ineffective.

Application of Spatial Transcriptomics in Digestive System Tumors

In the field of digestive system tumor research, spatial transcriptomics technologies are used to delve into the spatial structure and the spatial heterogeneity of tumors and to analyze the tumor microenvironment (TME) and the inter-cellular interactions within it by revealing gene expression in tumors. These technologies are also instrumental in the diagnosis, prognosis, and treatment of digestive system tumors. This review provides a concise introduction to spatial transcriptomics and summarizes recent advances, application prospects, and technical challenges of these technologies in digestive system tumor research. This review also discusses the importance of combining spatial transcriptomics with single-cell RNA sequencing (scRNA-seq), artificial intelligence, and machine learning in digestive system cancer research.

Unraveling Emerging Anal Cancer Clinical Biomarkers from Current Immuno-Oncogenomics Advances

Anal squamous cell carcinoma (ASCC) is a rare gastrointestinal malignancy associated with high-risk human papillomavirus (HPV) and is currently one of the fastest-growing causes of cancer incidence and mortality in developed countries. Although next-generation sequencing technologies (NGS) have revolutionized cancer and immuno-genomic research in various tumor types, a limited amount of clinical research has been developed to investigate the expression and the functional characterization of genomic data in ASCC. Herein, we comprehensively assess recent advancements in "omics" research, including a systematic analysis of genome-based studies, aiming to identify the most relevant ASCC cancer driver gene expressions and their associated signaling pathways. We also highlight the most significant biomarkers associated with anal cancer progression, gene expression of potential diagnostic biomarkers, expression of therapeutic drug targets, and emerging treatment opportunities. This review stresses the urgent need for developing target-specific therapies in ASCC. By illuminating the molecular characteristics and drug-target expression in ASCC, this study aims to provide insights for the development of precision medicine in anal cancer.

Optimized whole-genome sequencing workflow for tumor diagnostics in routine pathology practice

Two decades after the genomics revolution, oncology is rapidly transforming into a genome-driven discipline, yet routine cancer diagnostics is still mainly microscopy based, except for tumor type-specific predictive molecular tests. Pathology laboratories struggle to quickly validate and adopt biomarkers identified by genomics studies of new targeted therapies. Consequently, clinical implementation of newly approved biomarkers suffers substantial delays, leading to unequal patient access to these therapies. Whole-genome sequencing (WGS) can successfully address these challenges by providing a stable molecular diagnostic platform that allows detection of a multitude of genomic alterations in a single cost-efficient assay and facilitating rapid implementation, as well as by the development of new genomic biomarkers. Recently, the Whole-genome sequencing Implementation in standard Diagnostics for Every cancer patient (WIDE) study demonstrated that WGS is a feasible and clinically valid technique in routine clinical practice with a turnaround time of 11 workdays. As a result, WGS was successfully implemented at the Netherlands Cancer Institute as part of routine diagnostics in January 2021. The success of implementing WGS has relied on adhering to a comprehensive protocol including recording patient information, sample collection, shipment and storage logistics, sequencing data interpretation and reporting, integration into clinical decision-making and data usage. This protocol describes the use of fresh-frozen samples that are necessary for WGS but can be challenging to implement in pathology laboratories accustomed to using formalin-fixed paraffin-embedded samples. In addition, the protocol outlines key considerations to guide uptake of WGS in routine clinical care in hospitals worldwide.

Investigation of the potential effects of estrogen receptor modulators on immune checkpoint molecules

Immune checkpoints regulate the immune system response. Recent studies suggest that flavonoids, known as phytoestrogens, may inhibit the PD-1/PD-L1 axis. We explored the potential of estrogens and 17 Selective Estrogen Receptor Modulators (SERMs) as inhibiting ligands for immune checkpoint proteins (CTLA-4, PD-L1, PD-1, and CD80). Our docking studies revealed strong binding energy values for quinestrol, quercetin, and bazedoxifene, indicating their potential to inhibit PD-1 and CTLA-4. Quercetin and bazedoxifene, known to modulate EGFR and IL-6R alongside estrogen receptors, can influence the immune checkpoint functionality. We discuss the impact of SERMs on PD-1 and CTLA-4, suggesting that these SERMs could have therapeutic effects through immune checkpoint inhibition. This study highlights the potential of SERMs as inhibitory ligands for immune checkpoint proteins, emphasizing the importance of considering PD-1 and CTLA-4 inhibition when evaluating SERMs as therapeutic agents. Our findings open new avenues for cancer immunotherapy by exploring the interaction between various SERMs and immune checkpoint pathways.

Biomarkers of pembrolizumab efficacy in advanced anal squamous cell carcinoma: analysis of a phase II clinical trial and a cohort of long-term responders

BACKGROUND

Recent trials suggest that programmed cell death 1 (PD-1)-directed immunotherapy may be beneficial for some patients with anal squamous cell carcinoma and biomarkers predictive of response are greatly needed.

METHODS

This multicenter phase II clinical trial (NCT02919969) enrolled patients with metastatic or locally advanced incurable anal squamous cell carcinoma (n=32). Patients received pembrolizumab 200 mg every 3 weeks. The primary endpoint of the trial was objective response rate (ORR). Exploratory objectives included analysis of potential predictive biomarkers including assessment of tumor-associated immune cell populations with multichannel immunofluorescence and analysis of circulating tumor tissue modified viral-human papillomavirus DNA (TTMV-HPV DNA) using serially collected blood samples. To characterize the clinical features of long-term responders, we combined data from our prospective trial with a retrospective cohort of patients with anal cancer treated with anti-PD-1 immunotherapy (n=18).

RESULTS

In the phase II study, the ORR to pembrolizumab monotherapy was 9.4% and the median progression-free survival was 2.2 months. Despite the high level of HPV positivity observed with circulating TTMV-HPV DNA testing, the majority of patients had low levels of tumor-associated CD8+PD-1+ T cells on pretreatment biopsy. Patients who benefited from pembrolizumab had decreasing TTMV-HPV DNA scores and a complete responder's TTMV-HPV DNA became undetectable. Long-term pembrolizumab responses were observed in one patient from the trial (5.3 years) and three patients (2.5, 6, and 8 years) from the retrospective cohort. Long-term responders had HPV-positive tumors, lacked liver metastases, and achieved a radiological complete response.

CONCLUSIONS

Pembrolizumab has durable efficacy in a rare subset of anal cancers. However, despite persistence of HPV infection, indicated by circulating HPV DNA, most advanced anal cancers have low numbers of tumor-associated CD8+PD-1+ T cells and are resistant to pembrolizumab.

New-generation technologies for spatial tissue analysis, indispensable tools for deciphering intratumor heterogeneity in the development of antibody-drug conjugates and radio-immunoconjugates for cancer treatment

Technologies allowing in situ tissue molecular analysis of the "high-plex" type (>20 molecules per tissue section) are the 21st century inventions that are revolutionizing our knowledge of the biology of malignant tumors and many benign alterations. These technologies are based on specific probe labeling systems for the detection of tissue components [proteins, messenger RNA (mRNA)], as well as on detailed image analysis, combined with computational tools. We are synthetically presenting technologies based on image analysis, such as multiplex immunofluorescence (mIF), imaging mass cytometry (IMC), and multiplexed ion beam imaging (MIBI), as well as the ones not based on image analysis, such as multiplex in situ hybridizations (ISHs) using various principles. All of them are supported by powerful software which enable both tissue segmentation and data analysis. In the context of cancer treatment personalization, these technologies can reveal areas of tumor tissue and/or cellular subpopulations that are responsible for good or bad responses to anticancer drugs. Thus, they represent an unprecedented aid in the exploration of intratumor heterogeneity (ITH), which has already been shown to be one of the main reasons for the therapeutic failure of targeted anticancer treatments. The arrival of antibody-drug conjugates (ADCs) and radio-immunoconjugates (RICs) in the therapeutic arsenal in oncology imposes a deep exploration of molecular ITH, where technologies of spatial tissue analysis reveal an emerging category of biomarkers-spatial biomarkers.