Computational pathology: A survey review and the way forward

Computational Pathology (CPath) is an interdisciplinary science that augments developments of computational approaches to analyze and model medical histopathology images. The main objective for CPath is to develop infrastructure and workflows of digital diagnostics as an assistive CAD system for clinical pathology, facilitating transformational changes in the diagnosis and treatment of cancer that are mainly address by CPath tools. With evergrowing developments in deep learning and computer vision algorithms, and the ease of the data flow from digital pathology, currently CPath is witnessing a paradigm shift. Despite the sheer volume of engineering and scientific works being introduced for cancer image analysis, there is still a considerable gap of adopting and integrating these algorithms in clinical practice. This raises a significant question regarding the direction and trends that are undertaken in CPath. In this article we provide a comprehensive review of more than 800 papers to address the challenges faced in problem design all-the-way to the application and implementation viewpoints. We have catalogued each paper into a model-card by examining the key works and challenges faced to layout the current landscape in CPath. We hope this helps the community to locate relevant works and facilitate understanding of the field's future directions. In a nutshell, we oversee the CPath developments in cycle of stages which are required to be cohesively linked together to address the challenges associated with such multidisciplinary science. We overview this cycle from different perspectives of data-centric, model-centric, and application-centric problems. We finally sketch remaining challenges and provide directions for future technical developments and clinical integration of CPath. For updated information on this survey review paper and accessing to the original model cards repository, please refer to GitHub. Updated version of this draft can also be found from arXiv.

Contemporary Diagnostic Reporting for Prostatic Adenocarcinoma: Morphologic Aspects, Molecular Correlates, and Management Perspectives

The diagnosis and reporting of prostatic adenocarcinoma have evolved from the classic framework promulgated by Dr Donald Gleason in the 1960s into a complex and nuanced system of grading and reporting that nonetheless retains the essence of his remarkable observations. The criteria for the "Gleason patterns" originally proposed have been continually refined by consensuses in the field, and Gleason scores have been stratified into a patient-friendly set of prognostically validated and widely adopted Grade Groups. One product of this successful grading approach has been the opportunity for pathologists to report diagnoses that signal carefully personalized management, placing the surgical pathologist's interpretation at the center of patient care. At one end of the continuum of disease aggressiveness, personalized diagnostic care means to sub-stratify patients with more indolent disease for active surveillance, while at the other end of the continuum, reporting histologic markers signaling aggression allows sub-stratification of clinically significant disease. Whether contemporary reporting parameters represent deeper nuances of more established ones (eg, new criteria and/or quantitation of Gleason patterns 4 and 5) or represent additional features reported alongside grade (intraductal carcinoma, cribriform patterns of carcinoma), assessment and grading have become more complex and demanding. Herein, we explore these newer reporting parameters, highlighting the state of knowledge regarding morphologic, molecular, and management aspects. Emphasis is made on the increasing value and stakes of histopathologists' interpretations and reporting into current clinical risk stratification and treatment guidelines.

The presence of intraductal carcinoma of prostate is a risk factor for poor pathologic response in men with high-risk prostate cancer receiving neoadjuvant therapy

OBJECTIVE

To explore the potential association between the presence of intraductal carcinoma of the prostate (IDC-P) on biopsy and pathologic response of primary tumor to neoadjuvant therapy in patients with high-risk prostate cancer.

METHODS

Eighty-five patients with high-risk localized/locally advanced prostate cancer (CaP) who were given 6-month neoadjuvant therapies of androgen deprivation therapy plus docetaxel or abiraterone prior to radical prostatectomy in 2 prospective trials were included in this study. The presence of IDC-P in biopsy pathology was rereviewed by 2 experienced pathologists. Favorable pathologic response was defined as pathologic complete response or minimal residual disease <5 mm on whole-mount histopathology. Characteristics of clinical and biopsy pathology variables were included in univariate and multivariate logistic regression analyses to identify risk factors for the prediction of favorable pathologic response on final pathology.

RESULTS

IDC-P was identified to be present on biopsy pathology of 35 patients (41.2%) while favorable pathologic responses were confirmed in 25 patients (29.4%). Initial prostate-specific antigen (PSA) (OR 3.592, 95% CI 1.176-10.971, P = 0.025) and the presence of IDC-P on biopsy pathology (OR 3.837, 95% CI 1.234-11.930, P = 0.020) were found to be significantly associated with favorable pathologic response in multivariate logistic regression analysis.

CONCLUSION

IDC-P on biopsy pathology was found to be an independent risk factor to predict a poor pathology response of primary CaP to neoadjuvant therapies.

In-Depth Comparison of Genetic Variants Demonstrates a Close Relationship Between Invasive and Intraductal Components of Prostate Cancer

Intraductal carcinoma (IDC) of the prostate is often associated with concurrent high-grade invasive prostate cancer (PCa) and poor clinical outcomes. In this context, IDC is thought to represent the retrograde spread of invasive prostatic adenocarcinoma into the acini and ducts. Prior studies have demonstrated a concordance of PTEN loss and genomic instability between the IDC and high-grade invasive components of PCa, but larger genomic association studies to solidify our understanding of the relationship between these 2 lesions are lacking. Here, we evaluate the genomic relationship between duct-confined (high-grade prostatic intraepithelial neoplasia and IDC) and invasive components of high-grade PCa using genetic variants generated by whole exome sequencing. High-grade prostatic intraepithelial neoplasia and IDC were laser-microdissected, and PCa and nonneoplastic tissue was manually dissected from 12 radical prostatectomies. A targeted next-generation sequencing panel was used to identify disease-relevant variants. Additionally, the degree of overlap between adjacent lesions was determined by comparing exome-wide variants detected using whole exome sequencing data. Our results demonstrate that IDC and invasive high-grade PCa components show common genetic variants and copy number alterations. Hierarchical clustering of genome-wide variants suggests that in these tumors, IDC is more closely related to the high-grade invasive components of the tumor compared with high-grade prostatic intraepithelial neoplasia. In conclusion, this study reinforces the concept that, in the context of high-grade PCa, IDC likely represents a late event associated with tumor progression.

Prostate Pathology: What is New in the 2022 WHO Classification of Urinary and Male Genital Tumors?

In 2022, after a six-year interval, the International Agency for Research on Cancer (IARC) has published the 5th edition of the WHO Classification of Urinary and Male Genital Tumors, which provides a comprehensive update on tumor classification of the genitourinary system. This review article focuses on prostate carcinoma and underscores changes in the prostate chapter as well as those made across the entire series of the 5th edition of WHO Blue Books. Although no major alterations were made to this chapter, some of the most notable updates include restructure of contents and introduction of a new format; standardization of mitotic counts, genomic nomenclatures, and units of length; refined definition for the terms "variant", "subtype", and "histologic pattern"; reclassification of prostatic intraepithelial neoplasia (PIN)-like adenocarcinoma as a subtype of prostatic acinar adenocarcinoma; and recognition of treatment-related neuroendocrine prostatic carcinoma as a distinct tumor type. Evolving and unsettled issues related to grading of intraductal carcinoma of the prostate and reporting of tertiary Gleason pattern, the definition and prognostic significance of cribriform growth pattern, and molecular pathology of prostate cancer will also be covered in this review.

The modified International Society of Urological Pathology system improves concordance between biopsy and prostatectomy tumour grade

OBJECTIVES

To assess the concordance between biopsy and radical prostatectomy (RP) specimens using the 2005 Gleason score (GS) and the International Society of Urological Pathology (ISUP) 2014/World Health Organization 2016 modified system, accounting for the introduction of transperineal biopsy and pre-biopsy multiparametric magnetic resonance imaging (mpMRI).

PATIENTS AND METHODS

Between 2002 and 2019, we identified 2431 patients with paired biopsy and RP histopathology from a prospectively recorded and maintained prostate cancer database. Biopsy specimens were graded according to the 2005 GS or ISUP 2014 modified system, according to the year of diagnosis. Multivariable logistic regression analysis was conducted to retrospectively assess the impact of prostate-specific antigen (PSA), PSA density, age, pre-biopsy mpMRI, and biopsy method, on the rate of upgraded disease. The kappa coefficient was used to establish the degree of change in concordance between groups.

RESULTS

Overall, 24% of patients had upgraded disease and 8% of patients had downgraded disease when using the modified ISUP 2014 criteria. Agreement in the updated ISUP 2014 cohort was 68%, compared with 55% in the 2005 GS group, which was validated by a kappa coefficient that was good (k = 0.5 ± 0.4) and poor (k = 0.3 ± 0.1), respectively. In multivariable models, a change in grading system independently improved overall disease concordance (P = 0.02), and there were no other co-segregated patient or pathological factors such as PSA, total number of cores, maximum cancer length, biopsy route or the use of mpMRI that impacted this finding.

CONCLUSION

The 2014 ISUP modifed system improves overall concordance between biopsy and surgical specimens, and thus allows more accurate prognostication and management in high-grade disease, independent of more extensive prostate sampling and the use of mpMRI.

Computationally Derived Cribriform Area Index from Prostate Cancer Hematoxylin and Eosin Images Is Associated with Biochemical Recurrence Following Radical Prostatectomy and Is Most Prognostic in Gleason Grade Group 2

BACKGROUND

The presence of invasive cribriform adenocarcinoma (ICC), an expanse of cells containing punched-out lumina uninterrupted by stroma, in radical prostatectomy (RP) specimens has been associated with biochemical recurrence (BCR). However, ICC identification has only moderate inter-reviewer agreement.

OBJECTIVE

To investigate quantitative machine-based assessment of the extent and prognostic utility of ICC, especially within individual Gleason grade groups.

DESIGN, SETTING, AND PARTICIPANTS

A machine learning approach was developed for ICC segmentation using 70 RP patients and validated in a cohort of 749 patients from four sites whose median year of surgery was 2007 and with median follow-up of 28 mo. ICC was segmented on one representative hematoxylin and eosin RP slide per patient and the fraction of tumor area composed of ICC, the cribriform area index (CAI), was measured.

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS

The association between CAI and BCR was measured in terms of the concordance index (c index) and hazard ratio (HR).

RESULTS AND LIMITATIONS

CAI was correlated with BCR (c index 0.62) in the validation set of 411 patients with ICC morphology, especially those with Gleason grade group 2 cancer (n = 192; c index 0.66), and was less prognostic when patients without ICC were included (c index 0.54). A doubling of CAI in the group with ICC morphology was prognostic after controlling for Gleason grade, surgical margin positivity, preoperative prostate-specific antigen level, pathological T stage, and age (HR 1.19, 95% confidence interval 1.03-1.38; p = 0.018).

CONCLUSIONS

Automated image analysis and machine learning could provide an objective, quantitative, reproducible, and high-throughput method of quantifying ICC area. The performance of CAI for grade group 2 cancer suggests that for patients with little Gleason 4 pattern, the ICC fraction has a strong prognostic role.

PATIENT SUMMARY

Machine-based measurement of a specific cell pattern (cribriform; sieve-like, with lots of spaces) in images of prostate specimens could improve risk stratification for patients with prostate cancer. In the future, this could help in expanding the criteria for active surveillance.

Analysis of Serum Markers with Regard to Treatment Procedures in Advanced Stage Prostate Cancer Patients

Background

Biomarkers predicting the efficacy of treatment for locally limited prostate cancer are greatly needed. This knowledge could improve the classification of patients for different methods of treatment and enable better recognition of groups with higher risk of biological recurrence. We prospectively assessed serial blood levels of apoptotic biomarkers and correlated them with response to treatment and clinical factors.

Material/Methods

Blood was collected from 25 patients with prostate cancer before and after surgery, 16 healthy volunteers with benign prostatic hyperplasia (BPH), and 14 patients with metastasized disease. Immunoenzymatic methods were used to determine circulating apoptotic and inflammatory mediators, including tumor necrosis factor α (TNF-α), type I receptor (TNFRI), and type II receptor (TNFRII); FAS ligand (FasL); TNF-related apoptosis-inducing ligand (TRIAL); caspase 8 (Cas8); caspase 9 (Cas9); DNA methylation (metDNA); P-selectin; and high-sensitivity C-reactive protein. The total circulating fragments of cell-free DNA (cfDNA) were measured directly in serum.

Results

Peripheral serum prostate-specific antigen increased rapidly together with cfDNA. A negative correlation was noted between tumor volume and TNFRI and TNFRII. Postsurgery P-selectin level was decreased, and metDNA and TNFRII levels were increased. Three comparisons were made between patient groups: surgical vs. BPH; surgical vs. palliative; and palliative vs. BPH. TNFRI, TNFRII, metDNA, P-selectin, Cas8, and FasL were shown to have significant roles.

Conclusions

The study indicated significant roles for cfDNA, both TNF receptors, metDNA, and P-selectin as serum biomarkers in patients with prostate cancer.

Prostate cancer growth patterns beyond the Gleason score: entering a new era of comprehensive tumour grading

The Gleason grading system is one of the most important factors in clinical decision‐making for prostate cancer patients, and is entirely based on the classification of tumour growth patterns. In recent years it has become clear that some individual growth patterns themselves have independent prognostic value, and could be used for better personalised risk stratification. In this review we summarise recent literature on the clinicopathological value and molecular characteristics of individual prostate cancer growth patterns, and show how these, most particularly cribriform architecture, could alter treatment decisions for prostate cancer patients.

Cribriform growth pattern in lung adenocarcinoma: More aggressive and poorer prognosis than acinar growth pattern

The predictive value of prognosis based on the histopathological subtype is a critical criterion in the new classification of lung adenocarcinoma published in 2011 by the International Association for the Study of Lung Cancer (IASLC), the American Thoracic Society (ATS), and the European Respiratory Society (ERS) (IASLC/ATS/ERS). In this new classification, the differences of histopathology and prognosis are two considerable parameters to classify the subtypes of lung adenocarcinoma. Cribriform growth pattern is regarded as a variant of acinar growth pattern in lung adenocarcinoma, however, more and more studies pointed out that cribriform growth pattern is associated with more aggressive histopathological structures, higher proportion of recurrence rates, and shorter postoperative survival than acinar growth pattern. These features are similar to solid or micropapillary predominant adenocarcinoma. In this review, we summarized the clinicopathological features, prognosis, and genetic variations of cribriform growth pattern of lung adenocarcinoma, and provided a novel insight into the diagnosis and treatment of cribriform lung adenocarcinoma.

Isolated Intraductal Carcinoma of the Prostate in Prostatectomy Specimens: Report of 2 Cases and Review of the Literature

Intraductal carcinoma of the prostate (IDCp) is a distinct neoplastic entity, and although recognized for some time, it was included for the first time in the histologic classification of prostate cancer in the 2016 publication of World Health Organization. IDCp represents an intraductal or intra-acinar proliferation of malignant cells, with preservation of the basal cell layer. Even though IDCp is usually accompanied by a high-grade invasive component, low-grade invasive carcinoma can rarely be seen adjacent to the lesion. Even rarer is the incidence of isolated IDCp in needle biopsies, while a few such cases have been reported in prostatectomy specimens. We report 2 cases with isolated IDCp without any invasive component. A review of the literature is performed including the diagnostic challenges of IDCp and its morphologic mimics, immunohistochemical markers, molecular aspects, and prognostic implications. Even though it is not yet clear whether IDCp represents an intraductal spread of invasive cancer or a precursor of invasive carcinoma, the existence of isolated IDCp reinforces the idea that, at least in some of the cases, IDCp is a precancerous lesion. Further molecular studies need to be performed in order to clarify its pathogenesis.

Molecular Biomarkers in Localized Prostate Cancer: ASCO Guideline

PURPOSE

This guideline provides recommendations for available tissue-based prostate cancer biomarkers geared toward patient selection for active surveillance, identification of clinically significant disease, choice of postprostatectomy adjuvant versus salvage radiotherapy, and to address emerging questions such as the relative value of tissue biomarkers compared with magnetic resonance imaging.

METHODS

An ASCO multidisciplinary Expert Panel, with representatives from the European Association of Urology, American Urological Association, and the College of American Pathologists, conducted a systematic literature review of localized prostate cancer biomarker studies between January 2013 and January 2019. Numerous tissue-based molecular biomarkers were evaluated for their prognostic capabilities and potential for improving management decisions. Here, the Panel makes recommendations regarding the clinical use and indications of these biomarkers.

RESULTS

Of 555 studies identified, 77 were selected for inclusion plus 32 additional references selected by the Expert Panel. Few biomarkers had rigorous testing involving multiple cohorts and only 5 of these tests are commercially available currently: Oncotype Dx Prostate, Prolaris, Decipher, Decipher PORTOS, and ProMark. With various degrees of value and validation, multiple biomarkers have been shown to refine risk stratification and can be considered for select men to improve management decisions. There is a paucity of prospective studies assessing short- and long-term outcomes of patients when these markers are integrated into clinical decision making.

RECOMMENDATIONS

Tissue-based molecular biomarkers (evaluating the sample with the highest volume of the highest Gleason pattern) may improve risk stratification when added to standard clinical parameters, but the Expert Panel endorses their use only in situations in which the assay results, when considered as a whole with routine clinical factors, are likely to affect a clinical decision. These assays are not recommended for routine use as they have not been prospectively tested or shown to improve long-term outcomes-for example, quality of life, need for treatment, or survival. Additional information is available at www.asco.org/genitourinary-cancer-guidelines.