Pancancer analysis of the prognostic and immunological role of FANCD2: a potential target for carcinogenesis and survival

Recent evidence has shed light on the significant role of FANCD2 in cancer initiation, development, and progression. However, a comprehensive pan-cancer analysis of FANCD2 has been lacking. In this study, we have conducted a thorough investigation into the expression profiles and prognostic significance of FANCD2, as well as its correlation with clinicopathological parameters and immune cell infiltration, using advanced bioinformatic techniques. The results demonstrate that FANCD2 is significantly upregulated in various common cancers and is associated with prognosis. Notably, higher expression levels of FANCD2 are linked to poor overall survival, as indicated by Cox regression and Kaplan-Meier analyses. Additionally, we have observed a decrease in the methylation of FANCD2 DNA in some cancers, and this decrease is inversely correlated with FANCD2 expression. Genetic alterations in FANCD2 predominantly manifest as mutations, which are associated with overall survival, disease-specific survival, disease-free survival, and progression-free survival in certain tumor types. Moreover, FANCD2 exhibits a strong correlation with infiltrating cell levels, immune checkpoint genes, tumor mutation burden (TMB), and microsatellite instability (MSI). Enrichment analysis further highlights the potential impact of FANCD2 on Fanconi anemia (FA) pathway and cell cycle regulation. Through this comprehensive pan-cancer analysis, we have gained a deeper understanding of the functions of FANCD2 in oncogenesis and metastasis across different types of cancer.

Mucin phenotype and genetic alterations in non-V600E BRAF-mutated colorectal cancer

Colorectal cancer (CRC) is a heterogeneous disease that develops through stepwise accumulation of genetic alterations and progresses via several distinct pathways. However, the tumorigenesis of CRCs with BRAF non-V600E mutations remains unclear. Here, we aimed to elucidate the tumorigenesis of CRCs with BRAF non-V600E mutations, focusing on differences in mucin phenotype and genetic alterations between CRCs with non-V600E and V600E mutations. We investigated 201 patients with CRC and performed panel testing of 415 genes to identify BRAF mutations. Patients were classified into five mucin phenotypes - large-intestinal, small-intestinal, gastric, mixed, and unclassified - using immunohistochemistry for CD10, MUC2, MUC5AC, and MUC6. BRAF mutations were identified in 24 of 201 patients' samples, of which 13 (6.5%) had a V600E mutation (V600E-mutant) and 11 (5.5%) had non-V600E mutations (non-V600E-mutant). MUC5AC expression was significantly associated with V600E mutations (P = 0.040), while CD10 expression was significantly associated with non-V600E mutations (P = 0.010). The small-intestinal mucin phenotype was significantly associated with non-V600E mutations (P = 0.031), while the mixed mucin phenotype was significantly associated with V600E mutations (P = 0.027). Regarding genetic alterations, focusing on the WNT signaling pathway, APC mutation was significantly associated with non-V600E mutations (P < 0.001), while RNF43 mutation was significantly associated with V600E mutations (P = 0.020). Considering the differences in mucin phenotype and genetic alterations, different modes of tumorigenesis are assumed for CRC with BRAF V600E mutation and non-V600E mutations. These findings are important in understanding the biology and treatment strategies for BRAF-mutant CRC.

Molecular Determinants of Neurocognitive Deficits in Glioma: Based on 2021 WHO Classification

Cognitive impairment is a common feature among patients with diffuse glioma. The objective of the study is to investigate the relationship between preoperative cognitive function and clinical as well as molecular factors, firstly based on the new 2021 World Health Organization's updated classification of central nervous system tumors. A total of 110 diffuse glioma patients enrolled underwent preoperative cognitive assessments using the Mini-Mental State Examination and Montreal Cognitive Assessment. Clinical information was collected from medical records, and gene sequencing was performed to analyze the 18 most influenced genes. The differences in cognitive function between patients with and without glioblastoma were compared under both the 2016 and 2021 WHO classification of tumors of the central nervous system to assess their effect of differentiation on cognition. The study found that age, tumor location, and glioblastoma had significant differences in cognitive function. Several genetic alterations were significantly correlated with cognition. Especially, IDH, CIC, and ATRX are positively correlated with several cognitive domains, while most other genes are negatively correlated. For most focused genes, patients with a low number of genetic alterations tended to have better cognitive function. Our study suggested that, in addition to clinical characteristics such as age, histological type, and tumor location, molecular characteristics play a crucial role in cognitive function. Further research into the mechanisms by which tumors affect brain function is expected to enhance the quality of life for glioma patients. This study highlights the importance of considering both clinical and molecular factors in the management of glioma patients to improve cognitive outcomes.

Genomic and Transcriptomic Characterization of Gastric Cancer with Bone Metastasis

PURPOSE

Bone metastasis (BM) adversely affects the prognosis of gastric cancer (GC). We investigated molecular features and immune microenvironment that characterize GC with BM compared to GC without BM.

MATERIALS AND METHODS

Targeted DNA and whole transcriptome sequencing were performed using formalin-fixed paraffin-embedded primary tumor tissues (gastrectomy specimens) of 50 GC cases with distant metastases (14 with BM and 36 without BM). In addition, immunohistochemistry (IHC) for mucin-12 and multiplex IHC for immune cell markers were performed.

RESULTS

Most GC cases with BM had a histologic type of poorly cohesive carcinoma and showed worse overall survival (OS) than GC without BM (p < 0.05). GC with BM tended to have higher mutation rates in TP53, KDR, APC, KDM5A, and RHOA than GC without BM. Chief cell-enriched genes (PGA3, PGC, and LIPF), MUC12, MFSD4A, TSPAN7, and TRIM50 were upregulated in GC with BM compared to GC without BM, which was correlated with poor OS (p < 0.05). However, the expression of SERPINA6, SLC30A2, PMAIP1, and ITIH2 were downregulated in GC with BM. GC with BM was associated with PIK3/AKT/mTOR pathway activation, whereas GC without BM showed the opposite effect. The densities of helper, cytotoxic, and regulatory T cells did not differ between the two groups, whereas the densities of macrophages were lower in GC with BM (p < 0.05).

CONCLUSION

GC with BM had different gene mutation and expression profiles than GC without BM, and had more genetic alterations associated with a poor prognosis.

Obesity associated pancreatic ductal adenocarcinoma: Therapeutic challenges

Obesity is a prominent health issue worldwide and directly impacts pancreatic health, with obese individuals exhibiting a significant risk for increasing pancreatic ductal adenocarcinoma (PDAC). Several factors potentially explain the increased risk for the development of PDAC, including obesity-induced chronic inflammation within and outside of the pancreas, development of insulin resistance and metabolic dysfunction, promotion of immune suppression within the pancreas during inflammation, pre- and malignant stages, variations in hormones levels (adiponectin, ghrelin, and leptin) produced from the adipose tissue, and acquisition of somatic mutations in tumor once- and suppressor proteins critical for pancreatic tumorigenesis. In this manuscript, we will explore the broad impact of these obesity-induced risk factors on the development and progression of PDAC, focusing on changes within the tumor microenvironment (TME) as they pertain to prevention, current therapeutic strategies, and future directions for targeting obesity management as they relate to the prevention of pancreatic tumorigenesis.

Genetic alterations shape innate immune cells to foster immunosuppression and cancer immunotherapy resistance

Cancer immunotherapy, particularly immune checkpoint inhibitors, has opened a new avenue for cancer treatment following the durable clinical benefits. Despite the clinical successes across several cancer types, primary or acquired resistance might eventually lead to cancer progression in patients with clinical responses. Hence, to broaden the clinical applicability of these treatments, a detailed understanding of the mechanisms limiting the efficacy of cancer immunotherapy is needed. Evidence provided thus far has implicated immunosuppressive innate immune cells infiltrating the tumor microenvironment as key players in immunotherapy resistance. According to the available data, genetic alterations can shape the innate immune response to promote immunotherapy resistance and tumor progression. Herein, this review has discussed the current understanding of the underlying mechanisms where genetic alterations modulate the innate immune milieu to drive immunosuppression and immunotherapy resistance.

Asian variant intravascular large B-cell lymphoma with highly suspected central nervous system involvement: A case report

BACKGROUND

Intravascular large B-cell lymphoma (IVLBCL) is a rare subtype of extranodal lymphoma. In particular, the Asian variant of IVLBCL is characterized by hemophagocytic lymphohistiocytosis along with bone marrow involvement. However, central nervous system (CNS) involvement is uncommon in this variant compared to the Western variant. Here, we report a case of typical Asian variant IVLBCL with highly suspected CNS involvement and discuss the nature of the disease and its genetic aberration.

CASE SUMMARY

A 67-year-old female patient complained of gradually worsening cognitive impairment. While hospitalized, she developed a high fever and showed marked bicytopenia. Intracranial imaging revealed a suspected leptomeningeal disease. Although no malignant cells were found in the cerebrospinal fluid (CSF), the protein and lactate dehydrogenase levels in CSF were increased. Bone marrow examination revealed an increased number of hemophagocytic histiocytes, and ¹⁸F-fluorodeoxyglucose (FDG) positron emission tomography with computerized tomography scan revealed increased FDG uptake in both adrenal glands, the liver, and the right ethmoid sinus. A tissue biopsy showed atypical large lymphoid cells with prominent nucleoli in the vessels, and the tumor cells were positive for CD20, BCL2, BCL6, and IRF4/MUM1. In addition, targeted sequencing identified MYD88, TET2, and PIM1 mutations. Consequently, we diagnosed the patient with the Asian variant of IVLBCL with highly suspected CNS involvement.

CONCLUSION

Suspicion of IVLBCL and immediate diagnosis lead to timely treatment. Moreover, careful CNS examination at diagnosis is recommended.

Bladder preservation after neoadjuvant therapy - 2021 IBCN updates part 1

The morbidity associated with radical cystectomy (RC) for muscle-invasive bladder cancer (MIBC) has fueled investigations into the feasibility of bladder preservation strategies after a favorable clinical response to neoadjuvant therapy (NAT). Identifying optimal candidates for bladder preservation is predicated on our ability to identify tumors with inherent cisplatin sensitivity and accurately stage patients before and after NAT. In the present review, we evaluate the accuracy and limitations of contemporary staging modalities and investigate clinical outcomes in patients with MIBC who were managed with bladder preservation after NAT. Lastly, we discuss the predictive role of cisplatin-sensitizing DNA damage response (DDR) gene alterations as a foundational component to current prospective clinical trials evaluating bladder preservation in the setting of MIBC.

First record of partial albinism in the Critically Endangered Angelshark (Squatina squatina) (Linnaeus, 1758)

We report the first case of partial albinism in the Critically Endangered Angelshark, Squatina squatina. The encounter with this specimen took place while SCUBA diving on the beach of Tufia, located on the east coast of the island of Gran Canaria on April 2, 2021. This is also the first confirmed finding of an albino elasmobranch specimen in the Canary Island archipelago. This article is protected by copyright. All rights reserved.

Whole-Exome Sequencing Revealed the Mutational Profiles of Primary Central Nervous System Lymphoma

BACKGROUND

Primary central nervous system lymphoma (PCNSL) is a highly aggressive type of extranodal non-Hodgkin lymphoma, of which approximately 90% of the cases are diffuse large B-cell lymphoma (DLBCL). In recent years, the incidence of PCNSL has significantly increased in women and older men. Although advanced treatments such as high-dose methotrexate (HD-MTX) and targeted agents have been introduced, the prognosis of these patients remains poorer than those with other forms of non-Hodgkin's lymphoma.

METHODS

Twelve cases of Chinese PCNSL were analyzed to detect their genetic alterations using whole-exome sequencing (WES). We identified 448 potential somatic single nucleotide variants (SNVs) with a median of 12 SNVs per PCNSL sample and 35 small indels with potentially protein-changing features in 9 PCNSL samples.

RESULTS

We found that myeloid differentiation factor 88 (MYD88) had the highest mutation frequency, which affected the activity of the nuclear factor-κB (NF-κB) pathway. PCNSL samples with low-density lipoprotein receptor-related protein 1B (LRP1B) mutations had a higher mutation rate than samples with wild-type LRP1B. Polycystic kidney and hepatic disease 1 (PKHD1), the causal gene of autosomal recessive polycystic kidney disease (ARPKD), was identified in 2 PCNSL cases and exhibited missense mutations. Pathway analysis revealed enrichment in pathways associated with central carbon metabolism in cancer, renal cell carcinoma, nicotine addiction, bladder cancer, and long-term depression.

CONCLUSIONS

WES revealed significantly mutated genes associated with the molecular mechanisms of PCNSL, which could serve as therapeutic targets to improve patient outcomes.

In Vitro Site Directed Mutagenesis

Site-Directed Mutagenesis (SDM) allows for changes in the DNA sequence of plasmids using polymerase chain reaction (PCR). It is a reliable, accessible, and rapid method which is the common initial step of many biochemial or genetic experiments. Here we describe the various different forms of SDM before giving a detailed method for the introduction of substitutions, insertions, or deletions using a fast, ligation-free protocol, followed by colony PCR to screen for mutated sequences.

Fine-tuning of epithelial taste bud organoid to promote functional recapitulation of taste reactivity

Taste stem/progenitor cells from posterior mouse tongues have been used to generate taste bud organoids. However, the inaccessible location of taste receptor cells is observed in conventional organoids. In this study, we established a suspension-culture method to fine-tune taste bud organoids by apicobasal polarity alteration to form the accessible localization of taste receptor cells. Compared to conventional Matrigel-embedded organoids, suspension-cultured organoids showed comparable differentiation and renewal rates to those of taste buds in vivo and exhibited functional taste receptor cells and cycling progenitor cells. Accessible taste receptor cells enabled the direct application of calcium imaging to evaluate the taste response. Moreover, suspension-cultured organoids can be genetically altered. Suspension-cultured taste bud organoids harmoniously integrated with the recipient lingual epithelium, maintaining the taste receptor cells and gustatory innervation capacity. We propose that suspension-cultured organoids may provide an efficient model for taste research, including taste bud development, regeneration, and transplantation.

[The value of molecular testing of thyroid aspirates]

In the evaluation of thyroid nodules, cytopathology of thyroid fine-needle aspiration specimens plays a central role. Established classification schemes should be used. In the case of indeterminate cytology, additional molecular tests may be used. However, the stratification of indeterminate thyroid nodules into malignant and benign lesions based on molecular tests alone, apart from costly commercial assays from US vendors, has so far been clearly limited. Molecular testing of single genetic alterations that can confirm malignancy in papillary, poorly differentiated, and anaplastic thyroid carcinomas is helpful and relatively easy to perform. However, negative test results by no means exclude malignant neoplasia. Predictive markers for single entities (BRAF V600E, RET mutations and RET fusions) should be tested in all advanced thyroid carcinomas.

[Genetic dissection of the molecular mechanism of malignant lymphoma using advanced genomic technology]

Malignant lymphomas are a group of heterogeneous lymphoid malignancies, consisting of over 70 subtypes, which are classified according to their cell of origin. Classically, disease classification has been based on cellular morphology and immunophenotype. Due to the advancement of next-generation sequencing (NGS) technology, many comprehensive genomic studies have clarified the landscape of somatic alterations in these lymphomas, which has drastically improved our understanding of their molecular pathogenesis. Consequently, a new framework has been proposed for disease classification based on such somatic alterations and/or gene expression characteristic of each lymphoma subtype. Additionally, the results from the genomic studies have also established an important basis for the development of new targeted therapies and prognostic biomarkers. In the future, NGS-based gene panels will be covered by health insurance, and cancer precision medicine is expected to become more prevalent in this field. This paper outlines the analytical methods used in genomic studies by primarily focusing on NGS technology, and describes the results of major genomic and single-cell studies for various subtypes of malignant lymphoma.

[NGS-based multi-gene panel testing in hematological malignancies: diagnosis and prognostic prediction]

Diagnosis and classification of hematological diseases have been based on morphological and immunological findings, but the emergence of next-generation sequencing (NGS) technology has highlighted the importance of genomic alterations. With the advent of this novel technology, numerous genetic alterations have been identified in hematological malignancies. In fact, more than 300 genetic alterations have been listed in the latest WHO classification, such as NPM1 mutation, for the subcategorization of acute myeloid leukemia. In addition, increasing evidence has suggested that combining genetic information with clinical factors improves prognostic prediction in several hematological malignancies. Although NGS-based genomic profiling has been used to provide precision medicine in solid cancers, no comprehensive genomic profiling test for hematological diseases is covered by public health insurance both in Japan and abroad. Identification of targetable alterations is the main purpose of NGS-based genomic profiling in solid cancers, whereas genetic information is useful not only for treatment stratification but also for diagnosis and prognostic prediction. In addition, genetic profiles of solid and hematological malignancies are quite different. Therefore, the development of a comprehensive genomic profiling test for hematological disease is imperative. Here, we discuss the clinical utility of a comprehensive genomic profiling test for hematological malignancies with an emphasis on diagnosis and prognostic prediction.

Pan-cancer analysis reveals the expression, genetic alteration and prognosis of pyroptosis key gene GSDMD

BACKGROUND

Gasdermins (GSDMs)-mediated pyroptosis is widely involved in activating anti-tumor immunity and suppressing tumor growth. However, whether gasdermin D (GSDMD)-mediated pyroptosis affects patient prognosis in pan-cancer remains unknown.

METHODS

We performed analyses of the RNA expression, genetic alteration, prognosis and immune infiltration of GSDMD in pan-cancer. In order to explore the relationship between pyroptosis and tumors, we calculated the correlation between GSDMD and pyroptosis key genes in pan-cancer. We also investigated the enrichment pathway of GSDMD-related genes.

RESULTS

GSDMD was differentially expressed in the vast majority of cancer, and could be used as a prognostic marker in adrenocortical carcinoma (ACC), kidney renal clear cell carcinoma (KIRC), brain lower grade glioma (LGG), liver hepatocellular carcinoma (LIHC), skin cutaneous melanoma (SKCM) and rectum adenocarcinoma (READ). Strong evidence indicated the significant correlation of GSDMD with almost all immune checkpoints and immune cells. Pyroptosis-related genes strongly associated with GSDMD in ACC, KIRC, LGG, LIHC and SKCM, suggesting that GSDMD-mediated pyroptosis might play a critical role in the five cancers.

CONCLUSION

All the evidence supported the potential role of GSDMD-mediated pyroptosis in cancer. Our results provided new insights into GSDMD as a prognostic marker and potential therapeutic target for cancer.

[Genetic studies on lymphoma]

Lymphoma comprises a group of diseases characterized by neoplastic proliferation of mature B, T, and NK cells. This disease entity is widely recognized to be clinically, pathologically, molecularly, and genetically heterogeneous. The classification of lymphomas was classically based on morphology and immunology, but recent dramatic advances in next-generation sequencing technology have revealed various genetic alterations in lymphomas, which influenced the revision of the WHO classification in 2017. Accumulating evidence on genetic alterations has enabled the development of more accurate diagnostic strategies and prognostic markers. Moreover, these findings provide opportunities to exploit new therapeutics that target genetic alterations, which would facilitate the use of precision medicine in lymphomas. Here, we briefly review the fundamental methods of genetic analysis using next-generation sequencing technology and describe the entire scenario of genetic alterations, focusing on the recent major studies that have revealed various genetic alterations in each lymphoma subtype and present a detailed discussion of the results and methods.

Polo like kinase 1 expression in cervical cancer tissues generated from multiple detection methods

Background

Existing studies of PLK1 in cervical cancer had several flaws. The methods adopted by those studies of detecting PLK1 expression in cervical cancer were single and there lacks comprehensive evaluation of the clinico-pathological significance of PLK1 in cervical cancer.

Methods

A total of 303 cervical tissue samples were collected for in-house tissue microarrays. Immunohistochemistry was performed for evaluating PLK1 expression between cervical cancer (including cervical squamous cell carcinoma (CESC) and cervical adenocarcinoma) and non-cancer samples. The Expression Atlas database was searched for querying PLK1 expression in different cervical cancer cell lines and different tissues in the context of pan-cancer. Standard mean difference (SMD) was calculated and the summarized receiver's operating characteristics (SROC) curves were plotted for integrated tissue microarrays, exterior high-throughput microarrays and RNA sequencing data as further verification. The effect of PLK1 expression on the overall survival, disease-free survival and event-free survival of cervical cancer patients was analyzed through Kaplan Meier survival curves for cervical cancer patients from RNA-seq and GSE44001 datasets. The gene mutation and alteration status of PLK1 in cervical cancer was inspected in COSMIC and cBioPortal databases. Functional enrichment analysis was performed for genes correlated with PLK1 from aggregated RNA-seq and microarrays.

Results

A total of 963 cervical cancer samples and 178 non-cancer samples were collected from in-house tissue microarrays and exterior microarrays and RNA-seq datasets. The combined expression analysis supported overexpression of PLK1 in CESC, cervical adenocarcinoma and all types of cervical cancer (SMD = 1.59, 95%CI [0.56-2.63]; SMD = 2.99, 95%CI [0.75-5.24]; SMD = 1.57, 95% CI [0.85-2.29]) and the significant power of PLK1 expression in distinguishing CESC or all types of cervical cancer samples from non-cancer samples (AUC = 0.94, AUC = 0.92). Kaplan-Meier survival curves showed that the event-free survival rate of cervical cancer patients with higher expression of PLK1 was shorter than that of patients with lower PLK1 (HR = 2.020, P = 0.0197). Genetic alteration of PLK1 including missense mutation and mRNA low occurred in 6% of cervical cancer samples profiled in mRNA expression. Genes positively or negatively correlated with PLK1 were mainly assembled in pathways such as DNA replication, cell cycle, mismatch repair, Ras signaling pathway, melanoma, EGFR tyrosine kinase inhibitor resistance and homologous recombination (P < 0.05).

Conclusions

Here, we provided sufficient evidence of PLK1 overexpression in cervical cancer. The overexpression of PLK1 in cervical cancer and the contributory effect of it on clinical progression indicated the hopeful prospect of PLK1 as a biomarker for cervical cancer.

Clinical implications of HER2 mRNA expression and intrinsic subtype in refractory HER2-positive metastatic breast cancer treated with pan-HER inhibitor, poziotinib

INTRODUCTION

We explored clinical implication of intrinsic molecular subtype in human epidermal growth factor receptor 2 (HER2) + metastatic breast cancer (BC) with pan-HER inhibitor from a phase II clinical trial of poziotinib in refractory HER2+BC patients.

METHODS

For this translational research correlated with phase II clinical trial, we performed an nCounter expression assay, using gene panel including 50 genes for PAM50 prediction and targeted deep sequencing.

RESULTS

From 106 participants, we obtained 97 tumor tissues and analyzed gene expression in 91 of these samples. Of 91 HER2+BCs, 40 (44.0%) were HER2-enriched (E) intrinsic molecular subtype, 17 (18.7%) of Luminal A, 16 (17.6%) of Basal-like, 14 (15.4%) of Luminal B and 4 (4.4%) of Normal-like. HER2-E subtype was associated with hormone receptor negativity (odds ratio [OR] 2.93; p = 0.019), 3 + of HER2 immunohistochemistry(IHC) (OR 5.64; p = 0.001), high mRNA expression of HER2 (OR 14.43; p = 0.001) and copy number(CN) amplification of HER2 (OR 12.80; p = 0.005). In genetic alterations, alteration was more frequently observed in HER2-E subtype (OR 3.84; p = 0.022) but there was no association between PIK3CA alteration and HER2-E subtype (p = 0.655). In terms of drug efficacy, high mRNA expression of HER2 was the most powerful predictor of poziotinib response (median progression-free survival [PFS): 4.63 months [high] vs. 2.56 [low]; p < .001). In a combination prediction model, median PFS of intrinsic subtypes except Her2-E with high HER2 mRNA expression without PIK3CA genetic alteration was 6.83 months and that of the remaining group was 1.74 months (p < .001).

CONCLUSION

HER2-E subtype was associated with hormone receptor status, HER2 IHC, CN and mRNA expression and TP53 mutation. In survival analysis, the information of level of HER2 mRNA expression, intrinsic molecular subtype and PI3K pathway alteration would be independent predictors to poziotinib treatment. ClinicalTrials.gov identifier: NCT02418689.

[Genetic alterations and lymphoma]

Malignant lymphoma is a group of heterogeneous lymphoid malignancies with different clinical, histological, and molecular features. Although this disease had been subclassified mainly according to morphology and immune phenotype, accumulating evidence has demonstrated that distinct mutations, copy number alterations, and structural variations exist among each subtype of malignant lymphoma with the advent of next-generation sequencing. Based on these observations, various genetic alterations have been described in the recent WHO classification, such as MYC and BCL2 and/or BCL6 rearrangements, defining high-grade B-cell lymphoma as a new entity. In addition, several studies have reported that genetic profiling can improve the ability to predict patient prognosis solely based on clinical factors of lymphomas. Moreover, many attempts to develop anti-cancer agents targeting genetic alterations are ongoing. Therefore, genetic alterations can be exploited to develop better diagnostic and therapeutic strategies for the treatment of lymphomas. Here, we describe the entire picture of genetic alterations in lymphomas and clarify their similarities and differences among various subtypes, specifically focusing on their significance in diagnosis, prognostication, and treatment.

Genetic Alterations and Checkpoint Expression: Mechanisms and Models for Drug Discovery

In this chapter, we will sketch a story that begins with the breakdown of chromosome homeostasis and genomic stability. Genomic alterations may render tumor cells eternal life at the expense of immunogenicity. Although antitumor immunity can be primed through neoantigens or inflammatory signals, tumor cells have evolved countermeasures to evade immune surveillance and strike back by modulating immune checkpoint related pathways. At present, monoclonal antibody drugs targeting checkpoints like PD-1 and CTLA-4 have significantly prolonged the survival of a variety of cancer patients, and thus have marked a great achievement in the history of antitumor therapy. Nevertheless, this is not the end of the story. As the relationship between genomic alteration and checkpoint expression is being delineated though the advances of preclinical animal models and emerging technologies, novel checkpoint targets are on the way to be discovered.

Imaging phenotype using 18F-fluorodeoxyglucose positron emission tomography-based radiomics and genetic alterations of pancreatic ductal adenocarcinoma

PURPOSE

This study aimed to determine if major gene mutations including in KRAS, SMAD4, TP53, and CDKN2A were related to imaging phenotype using ¹⁸F-fluorodeoxyglucose (FDG) positron emission tomography (PET)-based radiomics in patients with pancreatic ductal adenocarcinoma (PDAC).

METHODS

Data on 48 PDAC patients with pretreatment FDG PET/CT who underwent genomic analysis of their tumor tissue were retrospectively analyzed. A total of 35 unique quantitative radiomic features were extracted from PET images, including imaging phenotypes such as pixel intensity, shape, and textural features. Targeted exome sequencing using a customized cancer panel was used for genomic analysis. To assess the predictive performance of genetic alteration using PET-based radiomics, areas under the receiver operating characteristic curve (AUC) were used.

RESULTS

Mutation frequencies were KRAS 87.5%, TP53 70.8%, SMAD4 25.0%, and CDKN2A 18.8%. KRAS gene mutations were significantly associated with low-intensity textural features, including long-run emphasis (AUC = 0.806), zone emphasis (AUC = 0.794), and large-zone emphasis (AUC = 0.829). SMAD4 gene mutations showed significant relationships with standardized uptake value skewness (AUC = 0.727), long-run emphasis (AUC = 0.692), and high-intensity textural features such as run emphasis (AUC = 0.775), short-run emphasis (AUC = 0.736), zone emphasis (AUC = 0.750), and short-zone emphasis (AUC = 0.725). No significant associations were seen between the imaging phenotypes and genetic alterations in TP53 and CDKN2A.

CONCLUSION

Genetic alterations of KRAS and SMAD4 had significant associations with FDG PET-based radiomic features in PDAC. PET-based radiomics may help clinicians predict genetic alteration status in a noninvasive way.

Ancillary Techniques in Cytologic Specimens Obtained from Solid Lesions of the Pancreas: A Review

Advanced methods of molecular characterization have elucidated the genetic, epigenetic, and proteomic alterations associated with the broad spectrum of pancreatic disease, particularly neoplasia. Next-generation sequencing, in particular, has revealed the genomic diversity among pancreatic ductal adenocarcinoma, neuroendocrine and acinar tumors, solid pseudopapillary neoplasm, and other pancreatico-biliary neoplasms. Differentiating these entities from one another by morphologic analysis alone may be challenging, especially when examining the small quantities of diagnostic material inherent to cytologic specimens. In order to enhance the sensitivity and specificity of pancreatic cytomorphology, multiple diagnostic, prognostic, and predictive ancillary tests have been and continue to be developed. Although a great number of such tests have been developed for evaluation of specimens collected from cystic lesions and strictures, ancillary techniques also play a significant role in the evaluation of cytologic specimens obtained from solid lesions of the pancreas. Furthermore, while some tests have been developed to differentiate diagnostic entities from one another, others have been developed to simply identify dysplasia and malignancy. Ancillary studies are particularly important in the subset of cases for which cytomorphologic analysis provides a result that is equivocal or insufficient to guide clinical management. Selection of appropriate ancillary testing modalities requires familiarity with both their methodology and the molecular basis of the pancreatic diseases for which testing is being performed.

Integrative immunologic and genomic characterization of brain metastasis from ovarian/peritoneal cancer

Brain metastasis from ovarian/peritoneal cancer is a rare disease that has a dismal prognosis. And genomic alterations and immune-profiling in primary ovarian/ peritoneal cancer and brain metastatic tumor tissues have not been fully elucidated. Multiplexed immunofluorescence and whole-exome sequencing of two matched brain metastatic tumor and primary ovarian/peritoneal cancer tissues were performed. The overall density of immune infiltrates in metastatic tissues (brain) was not significantly different from those in primary cancer tissues (case 1 primary: 2.12% and case 1 metastasis: 2.22%; case 2 primary: 1.70%, and case 2 metastasis: 3.46%). Of note, however, PD-L1 expression in the metastases was higher than that in the primary tumors. We found more non-silent mutations, cancer-related genes, loss of heterozygosity (LOH) and longer lengths of copy-number alterations (CNA) in brain metastases compared to primary ovarian/peritoneal cancers. We report immunologic and genomic profiles of primary ovarian/peritoneal cancer with brain metastasis that may not only provide useful information for understanding its pathogenesis, but also clues for further innovative therapeutic treatments for ovarian cancer.

Molecular genetics and therapeutic targets of pediatric low-grade gliomas

Pediatric low-grade gliomas (PLGGs) have relatively favorable prognosis and some resectable PLGGs, such as cerebellar pilocytic astrocytoma, can be cured by surgery alone. However, many PLGG cases are unresectable and some of them undergo tumor progression. Therefore, a multidisciplinary approach is necessary to treat PLGG patients. Recent genomic analysis revealed a broad genomic landscape underlying PLGG. Notably, the majority of PLGGs present MAPK pathway-associated genomic alterations and MAPK signaling-dependent tumor progression. Following preclinical evidence, many clinical trials based on molecular target therapy have been conducted on PLGG patients, some of whom exhibited durable response to target therapy. Here, we provide an overview of PLGG genetics and the evidence supporting the application of molecular target therapy in these patients.

Mutation analysis of therapy-related myeloid neoplasms

We analyzed the genetic mutation status of 13 patients with therapy-related myeloid neoplasms (t-MN). Consistent with previous reports, t-MN cells preferentially acquired mutations in TP53 and epigenetic modifying genes, instead of mutations in tyrosine kinase and spliceosome genes. Furthermore, we compared the mutation status of three t-MN cells with each of the initial lymphoid malignant cells, and identified common mutations among t-MN and the initial malignant cells in two patients. In a patient who developed chronic myelomonocytic leukemia (CMML) after follicular lymphoma (FL), TET2 mutation was identified in both CMML and FL cells. Notably, the TET2 mutation was also identified in peripheral blood cells in the disease-free period with the same allelic frequency as CMML and FL cells, but not in a germ-line control, indicating that the TET2 mutation occurred somatically in the initiating clone for both malignant cells. On the other hand, a germ-line MYB mutation was identified in a patient who developed myelodysplastic syndromes (MDS) after FL. These results suggest that germ-line deposition and clonal hematopoiesis are closely associated with t-MN susceptibility; however, further analysis is necessary to clarify the mechanism required to provide the initiating clone with lineage commitment and clonal expansion.

Integrated Oncogenomic Profiling of Copy Numbers and Gene Expression in Lung Adenocarcinomas without EGFR Mutations or ALK Fusion

Targeted therapies based on EGFR mutations or on the ALK fusion oncogene have become the standard treatment for certain patients with lung adenocarcinoma (LUAD). However, most LUAD patients have no EGFR mutation or ALK fusion, and their oncogenetic alterations remain to be characterized. Here we conducted an integrated analysis of public datasets to assess the genomic alterations of 23 highly lung cancer-associated genes. The copy numbers of these genes were measured in ten micro-dissected, paired tumors and normal lung tissues of LUAD patients without EGFR mutations or ALK fusion. The copy numbers of PTEN, RB1, HMGA2, and PTPRD were lower in tumors compared with those for normal tissues. Although there were reduced mRNA levels of PTEN and RB1 in tumors, there was a correlation between copy number and expression only for PTEN. In addition, analysis of the copy number alterations of these 23 genes revealed correlations between EMSY/CCND1, EMSY/PIK3CA, CCND1/CDKN2A, and CCND1/PIK3CA. Our exploration of integrated copy number and gene expression analysis gives priority to the PTEN-PIK3CA and RB1-CCND1 pathways in developing therapeutic strategies for LUAD patients without EGFR mutations or ALK fusion.

Central Precocious Puberty Caused by a Heterozygous Deletion in the MKRN3 Promoter Region

CONTEXT

Loss-of-function mutations in the coding region of MKRN3, a maternally imprinted gene at chromosome 15q11.2, are a common cause of familial central precocious puberty (CPP). Whether MKRN3 alterations in regulatory regions can cause CPP has not been explored to date. We aimed to investigate potential pathogenic variants in the promoter region of MKRN3 in patients with idiopathic CPP.

PATIENTS/METHODS

A cohort of 110 patients with idiopathic CPP was studied. Family history of precocious sexual development was present in 25%. Mutations in the coding region of MKRN3 were excluded in all patients. Genomic DNA was extracted from peripheral blood leukocytes, and 1,100 nucleotides (nt) of the 5'-regulatory region of MKRN3 were amplified and sequenced. Luciferase assays were performed in GT1-7 cells transiently transfected with plasmids containing mutated and wild-type MKRN3 promoter.

RESULTS

We identified a rare heterozygous 4-nt deletion (c.-150_-147delTCAG; -38 to -41 nt upstream to the transcription start site) in the proximal promoter region of MKRN3 in a girl with CPP. In silico analysis predicted that this deletion would lead to the loss of a binding site for a downstream res-ponsive element antagonist modulator (DREAM), a potential transcription factor for MKRN3 and GNRH1 expression. Luciferase assays demonstrated a significant reduction of MKRN3 promoter activity in transfected cells with a c.-150_- 147delTCAG construct plasmid in both homozygous and heterozygous states when compared with cells transfected with the corresponding wild-type MKRN3 promoter region.

CONCLUSION

A rare genetic alteration in the regulatory region of MKRN3 causes CPP.

Pediatric acute myeloid leukemia with genetic alterations

Annually, it is estimated that approximately 150-200 children aged 0-16 years are diagnosed with acute myeloid leukemia (AML). In Japan, clinical studies with ANLL91, AML99, CCLSG-AML9805, and JPLSG-AML05 protocols were performed historically, and the risk stratification with a combination of chemotherapy and hematopoietic stem cell transplantation resulted in the improvement of clinical outcomes. Regarding the onset of pediatric AML at the molecular level, mutations in FLT3-ITD or KIT (Class I mutation) showed a poor prognosis, but the ratio of mutations in Class III-V genes was smaller than that in adult AML. In contrast, several pediatric AML cases are complicated due to chromosome fragility syndrome or congenital bone marrow failure syndrome. To improve the clinical outcomes, clinical application of next generation sequencing may allow for personalized therapy in each patient in the future.

Molecular Patterns and Biology of HPV-Associated HNSCC

Head and neck cancer is the sixth most common cancer worldwide. The large majority are squamous cell carcinomas (HNSCC) that develop in the mucosal linings of the upper aerodigestive tract. These tumors develop either by exogenous carcinogen exposure (smoking, alcohol drinking) or by human papillomavirus (HPV) infection, particularly those in the oropharynx (OPSCC). HPV-positive (HPV+ve) and HPV-negative (HPV-ve) OPSCC are considered different disease entities. HPV+ve tumors are different at the molecular level and likely as a consequence have a much more favorable prognosis than HPV-ve tumors, despite their generally advanced stage at presentation. In general, HNSCCs develop in precancerous mucosal changes, and the apparent lack of precancerous HPV+ve mucosal changes is therefore remarkable. In this Chapter, head and neck carcinogenesis is discussed and the molecular differences between HPV+ve and HPV-ve tumors are outlined.

Genetic alteration regulated by microRNAs in biliary tract cancers

Biliary tract cancers (BTCs) constitute a relatively rare but highly malignant class of tumors with poor prognosis including gallbladder cancer, intra- and extra-hepatic cholangiocarcinoma. Recently, accumulated evidences have demonstrated that deregulated expression of microRNAs (miRNAs) is closely associated with the development, invasion, metastasis and prognosis of different cancers including BTCs. MiRNAs comprise an endogenously expressed and highly evolutionarily conserved group of small, non-coding, single-stranded RNAs which negatively regulate target genes expression by means of combining with 3' untranslated region (UTR) of corresponding mRNAs at the post-transcriptional level with significant roles in various fundamental cellular procedures including cell proliferation, differentiation, migration, cell cycle control and apoptosis. Recent studies have indicated that miRNAs could function as novel tumor-promoting genes or tumor suppressor genes to act as potential therapeutic targets in anticancer treatment because the genetic alteration regulated by miRNAs could result in tumorigenesis and tumor inhibition. Anomalous miRNAs expression patterns, acting as phenotypic signatures of distinct cancers, are promising to be used as diagnostic, prognostic, predictive biomarkers. In this review, we summarize the current findings from the studies about potential genetic alteration regulated by miRNAs and their roles in BTCs.

Pathogenesis of cholangiocarcinoma: From genetics to signalling pathways

Cholangiocarcinoma (CCA) is a malignant tumour of bile duct epithelial cells with dismal prognosis and rising incidence. Chronic inflammation resulting from liver fluke infection, hepatitis and other inflammatory bowel diseases is a major contributing factor to cholangiocarcinogenesis, likely through accumulation of serial genetic and epigenetic alterations resulting in aberration of oncogenes and tumour suppressors. Recent studies making use of advances in high-throughput genomics have revealed the genetic landscape of CCA, greatly increasing our understanding of its underlying biology. A series of highly recurrent mutations in genes such as TP53, KRAS, SMAD4, BRAF, MLL3, ARID1A, PBRM1 and BAP1, which are known to be involved in cell cycle control, cell signalling pathways and chromatin dynamics, have led to investigations of their roles, through molecular to mouse modelling studies, in cholangiocarcinogenesis. This review focuses on the landscape genetic alterations in CCA and its functional relevance to the formation and progression of CCA.

Immunohistochemical markers in lymphoid malignancies: Protein correlates of molecular alterations

Histomorphology, immunohistochemistry (IHC), and genetics are essential tools for the evaluation and classification of lymphoid malignancies. Advances in diagnostic techniques include the development of immunohistochemical assays that can serve as surrogates for genetic tests. We review the performance of a select subset of assays that detect the aberrant expression of onco-proteins secondary to chromosomal translocations (MYC; BCL2), somatic mutations (BRAF V600E; NOTCH1), and gene copy number gains (CD274 (encoding PD-L1); PDCD1LG2 (encoding PD-L2)) in fixed tissue biopsy sections. We discuss the limitations of IHC, but also its primary advantage over genetics; specifically, its ability to assess the final, common phenotypic consequences of a multitude of genetic and non-genetic events that influence protein expression. The information provided by IHC and genetic testing are thus intimately related; surgical pathologists will increasingly need to interpret and integrate the results of both to provide a comprehensive assessment of tumor biology and guide therapy.

A synonymous genetic alteration of LMX1B in a family with nail-patella syndrome

The gene responsible for nail-patella syndrome, LMX1B, has recently been identified on chromosome 9q. Here we present a patient with nail-patella syndrome and an autosomal dominant pattern of inheritance. A 17-year-old girl visited our clinic for the evaluation and treatment of proteinuria. She had dystrophic nails, palpable iliac horns, and hypoplastic patellae. Electron microscopy of a renal biopsy showed irregular thickening of the glomerular basement membrane. A family history over three generations revealed five affected family members. Genetic analysis found a change of TCG to TCC, resulting in a synonymous alteration at codon 219 in exon 4 of the LMX1B gene in two affected family members. The same alteration was not detected in an unaffected family member. This is the first report of familial nail-patella syndrome associated with an LMX1B in Korea mutation, However, we can not completely rule out the possibility that the G-to-C change may be a single nucleotide polymorphism as this genetic mutation cause no alteration in amino acid sequence of LMX1B.