The role of the pathology department in the preanalytical phase of molecular analyses

Breast cancer in northern Peru: molecular subtypes and HER2 low

This study aimed to understand the immunohistochemical profile of breast cancer and to identify the HER2 low subgroup in the northern macro-region of Peru. A cross-sectional study was conducted in 1176 patients from the Regional Institute of Neoplastic Diseases Northern Peru, from January 2016 to December 2023. We analyzed the data (age, histological type, grade and complementary results), with frequencies and percentages. The profile corresponded to: luminal B (45.6%); luminal A (24.7%); triple negative (18.2%); and HER2 positive non luminal (11.5%). In addition, 215 patients presented HER2 low (25.1% of those previously considered negative). This study provides evidence that the subtyping of breast cancer has changed, being luminal B the most frequent. It is essential to involve health policies to acquire targeted therapies considering HER2 low patients. Motivation for the study. Molecular classification of breast cancer allows the use of targeted treatments. Information on this profile in the northern macroregion of Peru is unknown. In addition, new therapies have appeared for a subgroup of patients. Main findings. In this study, the most frequent molecular subtypes were: luminal B, luminal A, triple negative and non-luminal HER2. Also, 18.3% of patients had low HER2 expression. Implications. Health policies should be aligned with scientific advances, to guarantee targeted therapies and to update the information in health manuals or protocols.

The neurobiology of SARS-CoV-2 infection

Worldwide, over 694 million people have been infected with SARS-CoV-2, with an estimated 55-60% of those infected developing COVID-19. Since the beginning of the pandemic in December 2019, different variants of concern have appeared and continue to occur. With the emergence of different variants, an increasing rate of vaccination and previous infections, the acute neurological symptomatology of COVID-19 changed. Moreover, 10-45% of individuals with a history of SARS-CoV-2 infection experience symptoms even 3 months after disease onset, a condition that has been defined as 'post-COVID-19' by the World Health Organization and that occurs independently of the virus variant. The pathomechanisms of COVID-19-related neurological complaints have become clearer during the past 3 years. To date, there is no overt - that is, truly convincing - evidence for SARS-CoV-2 particles in the brain. In this Review, we put special emphasis on discussing the  methodological difficulties of viral detection in CNS tissue and discuss immune-based (systemic and central) effects contributing to COVID-19-related CNS affection. We sequentially review the reported changes to CNS cells in COVID-19, starting with the blood-brain barrier and blood-cerebrospinal fluid barrier - as systemic factors from the periphery appear to primarily influence barriers and conduits - before we describe changes in brain parenchymal cells, including microglia, astrocytes, neurons and oligodendrocytes as well as cerebral lymphocytes. These findings are critical to understanding CNS affection in acute COVID-19 and post-COVID-19 in order to translate these findings into treatment options, which are still very limited.

FFPE-Based NGS Approaches into Clinical Practice: The Limits of Glory from a Pathologist Viewpoint

The introduction of next-generation sequencing (NGS) in the molecular diagnostic armamentarium is deeply changing pathology practice and laboratory frameworks. NGS allows for the comprehensive molecular characterization of neoplasms, in order to provide the best treatment to oncologic patients. On the other hand, NGS raises technical issues and poses several challenges in terms of education, infrastructures and costs. The aim of this review is to give an overview of the main NGS sequencing platforms that can be used in current molecular diagnostics and gain insights into the clinical applications of NGS in precision oncology. Hence, we also focus on the preanalytical, analytical and interpretative issues raised by the incorporation of NGS in routine pathology diagnostics.

Detection methods for SARS-CoV-2 in tissue

BACKGROUND

Analyses for the presence of SARS-CoV‑2 in the tissues of COVID-19 patients is important in order to improve our understanding of the disease pathophysiology for interpretation of diagnostic histopathological findings in autopsies, biopsies, or surgical specimens and to assess the potential for occupational infectious hazard.

MATERIAL AND METHODS

In this review we identified 136 published studies in PubMed's curated literature database LitCovid on SARS-CoV‑2 detection methods in tissues and evaluated them regarding sources of error, specificity, and sensitivity of the methods, taking into account our own experience.

RESULTS

Currently, no sufficiently specific histomorphological alterations or diagnostic features for COVID-19 are known. Therefore, three approaches for SARS-CoV‑2 detection are used: RNA, proteins/antigens, or morphological detection by electron microscopy. In the preanalytical phase, the dominant source of error is tissue quality, especially the different intervals between sample collection and processing or fixation (and its duration) and specifically the interval between death and sample collection in autopsies. However, this information is found in less than half of the studies (e.g., in only 42% of autopsy studies). Our own experience and first studies prove the significantly higher sensitivity and specificity of RNA-based detection methods compared to antigen or protein detection by immunohistochemistry or immunofluorescence. Detection by electron microscopy is time consuming and difficult to interpret.

CONCLUSIONS

Different methods are available for the detection of SARS-CoV‑2 in tissue. Currently, RNA detection by RT-PCR is the method of choice. However, extensive validation studies and method harmonization are not available and are absolutely necessary.

Pathologists at the Leading Edge of Optimizing the Tumor Tissue Journey for Diagnostic Accuracy and Molecular Testing

OBJECTIVES

Tumor biomarker analyses accompanying immuno-oncology therapies are coupled with a tumor tissue journey aiming to guide tissue procurement and allow for accurate diagnosis and delivery of test results. The engagement of pathologists in the tumor tissue journey is essential because they are able to link the preanalytic requirements of this process with pathologic evaluation and clinical information, ultimately influencing treatment decisions for patients with cancer. The aim of this review is to provide suggestions on how cancer diagnosis and the delivery of molecular test results may be optimized, based on the needs and available resources of institutions, by placing the tumor tissue journey under the leadership of pathologists.

METHODS

Literature searches on PubMed and personal experience provided the necessary material to satisfy the objectives of this review.

RESULTS

Pathologists are usually involved across many steps of the tumor tissue journey and have the requisite knowledge to ensure its efficiency.

CONCLUSIONS

The expansion of oncology diagnostic testing emphasizes the need for pathologists to acquire a leadership role in the multidisciplinary effort to optimize the accuracy, completeness, and delivery of diagnoses guiding personalized treatments.

Recommendations for streamlining precision medicine in breast cancer care in Latin America

Background

The incidence of breast cancer (BC) in LMICs has increased by more than 20% within the last decade. In areas such as Latin America (LA), addressing BC at national levels evoke discussions surrounding fragmented care, limited resources, and regulatory barriers. Precision Medicine (PM), specifically companion diagnostics (CDx), links disease diagnosis and treatment for better patient outcomes. Thus, its application may aid in overcoming these barriers.

Recent findings

A panel of LA experts in fields related to BC and PM were provided with a series of relevant questions to address prior to a multi‐day conference. Within this conference, each narrative was edited by the entire group, through numerous rounds of discussion until a consensus was achieved. The panel proposes specific, realistic recommendations for implementing CDx in BC in LA and other LMIC regions. In these recommendations, the authors strived to address all barriers to the widespread use and access mentioned previously within this manuscript.

Conclusion

This manuscript provides a review of the current state of CDx for BC in LA. Of most importance, the panel proposes practical and actionable recommendations for the implementation of CDx throughout the Region in order to identify the right patient at the right time for the right treatment.

[Methods of SARS-CoV-2 detection in tissue]

BACKGROUND

Analyses for the presence of SARS-CoV‑2 in the tissues of COVID-19 patients is important in order to improve our understanding of the disease pathophysiology for interpretation of diagnostic histopathological findings in autopsies, biopsies, or surgical specimens and to assess the potential for occupational infectious hazard.

MATERIAL AND METHODS

In this review we identified 136 published studies in PubMed's curated literature database LitCovid on SARS-CoV‑2 detection methods in tissues and evaluated them regarding sources of error, specificity, and sensitivity of the methods, taking into account our own experience.

RESULTS

Currently, no sufficiently specific histomorphological alterations or diagnostic features for COVID-19 are known. Therefore, three approaches for SARS-CoV‑2 detection are used: RNA, proteins/antigens, or morphological detection by electron microscopy. In the preanalytical phase, the dominant source of error is tissue quality, especially the different intervals between sample collection and processing or fixation (and its duration) and specifically the interval between death and sample collection in autopsies. However, this information is found in less than half of the studies (e.g., in only 42% of autopsy studies). Our own experience and first studies prove the significantly higher sensitivity and specificity of RNA-based detection methods compared to antigen or protein detection by immunohistochemistry or immunofluorescence. Detection by electron microscopy is time consuming and difficult to interpret.

CONCLUSIONS

Different methods are available for the detection of SARS-CoV‑2 in tissue. Currently, RNA detection by RT-PCR is the method of choice. However, extensive validation studies and method harmonization are not available and are absolutely necessary.

Approach to the Adult Acute Lymphoblastic Leukemia Patient

During recent decades, understanding of the molecular mechanisms of acute lymphoblastic leukemia (ALL) has improved considerably, resulting in better risk stratification of patients and increased survival rates. Age, white blood cell count (WBC), and specific genetic abnormalities are the most important factors that define risk groups for ALL. State-of-the-art diagnosis of ALL requires cytological and cytogenetical analyses, as well as flow cytometry and high-throughput sequencing assays. An important aspect in the diagnostic characterization of patients with ALL is the identification of the Philadelphia (Ph) chromosome, which warrants the addition of tyrosine kinase inhibitors (TKI) to the chemotherapy backbone. Data that support the benefit of hematopoietic stem cell transplantation (HSCT) in high risk patient subsets or in late relapse patients are still questioned and have yet to be determined conclusive. This article presents the newly published data in ALL workup and treatment, putting it into perspective for the attending physician in hematology and oncology.

Avoiding non-contributive molecular results in cancer samples: proposal of a score-based approach for sample choice

Mutational analyses have become crucial for therapeutic choices in patients with advanced lung cancer, colorectal cancer and melanoma. Short turnaround times for molecular analyses are necessary to match the patient's therapeutic management. Non-contributive molecular analyses may increase the delay in reaching a relevant mutational status. We attempted to identify criteria in samples associated with non-contributive molecular results to better anticipate them and select samples with contributive analyses. We compared several criteria such as cancer type, sample type, organ of origin and percentage of tumour cells between samples with non-contributive or contributive EGFR, KRAS, NRAS and BRAF mutation analyses. Among two sets of 3367 and 554 tumour samples analysed in 2015-2017 and 2018, respectively, 11.7% and 15.7% of sample analyses were non-contributive for at least one oncogene. Lung cancer and melanoma cancer subtypes [odds ratio (OR)=7.2], cytological (OR=1.8) or bone samples (OR=8.5) and a percentage of tumour cells ≤20% (OR=41.4) were significantly associated with non-contributive results. By combining these parameters in a scoring system, we were able to predict the contributive or non-contributive result of a molecular analysis with sensitivity and specificity higher than 80% in a validation set of samples. Predicting the contributive or non-contributive result of a molecular analysis is feasible in samples on the basis of simple features. A combination of these features could be used to better choose samples to analyse in order to reduce the rate of non-contributive molecular results and related treatment delays and costs in patients with advanced cancers.

Evaluation of Formalin Fixation for Tissue Biopsies Using Shear Wave Laser Speckle Imaging System

Chemical fixation is the slowest and often the most uncontrolled step in the multi-step process of preparing tissue for histopathology. In order to reduce the time from taking a core needle biopsy to making a diagnosis, a new approach is proposed that optically monitors the common formalin fixation process. A low-cost and highly-sensitive laser speckle imaging technique is developed to measure shear wave velocity in a biospecimen as small as 0.5 mm in thickness submerged in millifluidic channels. Shear wave velocity, which is the indicator of tissue mechanical property and induced by piezoelectric-actuation, was monitored using gelatin phantom and chicken breast during fixation, as well as post-fixed liver and colon tissues from human. Fixation levels in terms of shear wave velocity increased by approximately 271.0% and 130.8% in gelatin phantom and chicken breast, respectively, before reaching the plateaus at 10.91 m/s and 7.88 m/s. Within these small specimens, the plateaus levels and times varied with location of measurement, and between gelatin and chicken breast. This optical-based approach demonstrates the feasibility of fine-tuning preanalytical variables, such as fixation time, for a rapid and accurate histopathological evaluation; provides a quality metric during the tissue preparation protocol performed in most pathology labs; and introduces the millifluidic chamber that can be engineered to be a future disposable device that automates biopsy processing and imaging.