Linking the ovarian cancer transcriptome and immunome

<p>Abstract</p> <p>Background</p> <p>Autoantigens have been reported in a variety of tumors, providing insight into the interplay between malignancies and the immune response, and also giving rise to novel diagnostic and therapeutic concepts. Why certain tumor-associated proteins induce an immune response remains largely elusive.</p> <p>Results</p> <p>This paper analyzes the proposed link between increased abundance of a protein in cancerous tissue and the increased potential of the protein for induction of a humoral immune response, using ovarian cancer as an example. Public domain data sources on differential gene expression and on autoantigens associated with this malignancy were extracted and compared, using bioinformatics analysis, on the levels of individual genes and proteins, transcriptional coregulation, joint functional pathways, and shared protein-protein interaction networks. Finally, a selected list of ovarian cancer-associated, differentially regulated proteins was tested experimentally for reactivity with antibodies prevalent in sera of ovarian cancer patients.</p> <p>Genes reported as showing differential expression in ovarian cancer exhibited only minor overlap with the public domain list of ovarian cancer autoantigens. However, experimental screening for antibodies directed against antigenic determinants from ovarian cancer-associated proteins yielded clear reactions with sera.</p> <p>Conclusion</p> <p>A link between tumor protein abundance and the likelihood of induction of a humoral immune response in ovarian cancer appears evident.</p

Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy.

MotivationMultiple biological clocks govern a healthy pregnancy. These biological mechanisms produce immunologic, metabolomic, proteomic, genomic and microbiomic adaptations during the course of pregnancy. Modeling the chronology of these adaptations during full-term pregnancy provides the frameworks for future studies examining deviations implicated in pregnancy-related pathologies including preterm birth and preeclampsia.ResultsWe performed a multiomics analysis of 51 samples from 17 pregnant women, delivering at term. The datasets included measurements from the immunome, transcriptome, microbiome, proteome and metabolome of samples obtained simultaneously from the same patients. Multivariate predictive modeling using the Elastic Net (EN) algorithm was used to measure the ability of each dataset to predict gestational age. Using stacked generalization, these datasets were combined into a single model. This model not only significantly increased predictive power by combining all datasets, but also revealed novel interactions between different biological modalities. Future work includes expansion of the cohort to preterm-enriched populations and in vivo analysis of immune-modulating interventions based on the mechanisms identified.Availability and implementationDatasets and scripts for reproduction of results are available through: https://nalab.stanford.edu/multiomics-pregnancy/.Supplementary informationSupplementary data are available at Bioinformatics online

Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy

Motivation Multiple biological clocks govern a healthy pregnancy. These biological mechanisms produce immunologic, metabolomic, proteomic, genomic and microbiomic adaptations during the course of pregnancy. Modeling the chronology of these adaptations during full-term pregnancy provides the frameworks for future studies examining deviations implicated in pregnancy-related pathologies including preterm birth and preeclampsia. Results We performed a multiomics analysis of 51 samples from 17 pregnant women, delivering at term. The datasets included measurements from the immunome, transcriptome, microbiome, proteome and metabolome of samples obtained simultaneously from the same patients. Multivariate predictive modeling using the Elastic Net (EN) algorithm was used to measure the ability of each dataset to predict gestational age. Using stacked generalization, these datasets were combined into a single model. This model not only significantly increased predictive power by combining all datasets, but also revealed novel interactions between different biological modalities. Future work includes expansion of the cohort to preterm-enriched populations and in vivo analysis of immune-modulating interventions based on the mechanisms identified. Availability and implementation Datasets and scripts for reproduction of results are available through: Https://nalab.stanford.edu/multiomics-pregnancy/

The peculiarities of gene expression of medullary breast carcinoma tumor-associated antigens in different types of breast tumors

Aim. To investigate gene expression profile of human medullary breast carcinoma’s tumor-associated antigens in different histological types of breast tumors. To analyze a correlation between alterations in gene expression level and induction of immune response against the corresponding antigens. Methods. Real-time polymerase chain reaction. Results. Differential gene expression profile of 6 (RAD50, HMGN2, RBPJ, PABPC4, BRAP, DEK) medullary breast carcinoma tumor-associated antigens have been revealed in breast tumors of different histological types. Correlation between changes in tumor-associated antigens gene expression level and induction of immune response has not been found. Conclusions. The genes of human medullary breast carcinoma tumor-associated antigens with differential expression profile in different histological types of breast tumors are potential diagnostic markers of breast cancer. Alteration of tumor-associated antigens gene expression level is not a prelude to an immune response against their corresponding protein products. Keywords: medullary breast carcinoma, tumor-associated antigens, immunoreactivity.Мета. Дослідити особливості експресії генів дев’яти пухлиноасоційованих антигенів медулярної карциноми молочної залози (МКМЗ) у пухлинах молочної залози різних гістологічних типів і проаналізувати можливість існування кореляції між змінами в рівні експресії генів та наявністю імунної відповіді проти відповідних антигенів. Методи. Полімеразна ланцюгової реакції у режимі реального часу. Результати. Виявлено диференційний профіль експресії шести (RAD50, HMGN2, RBPJ, PABPC4, BRAP і DEK) з дев’яти досліджуваних генів у різних гістологічних типах пухлин молочної залози. Кореляції між змінами в рівні експресії генів та наявністю імунної відповіді проти відповідних антигенів не встановлено. Висновки. Гени RAD50, HMGN2, RBPJ, PABPC4, BRAP і DEK антигенів МКМЗ, які мають диференційний профіль експресії у різних гістологічних типах пухлин молочної залози, є потенційними діагностичними маркерами раку молочної залози. Встановлено, що зміна експресії досліджених генів не є обов’язковою умовою виникнення імунної відповіді проти їхніх білкових продуктів. Ключові слова: карцинома молочної залози, пухлиноасоційовані антигени, імунореактивність.Цель. Исследовать особенности экспрессии генов девяти опухоль-ассоциированных антигенов медуллярной карциномы молочной железы (МКМЖ) в опухолях молочной железы разных гистологических типов и проанализировать возможность существования корреляции между изменениями в уровне экспрессии генов и наличием иммунного ответа против соответствующих антигенов. Методы. Уровень экспрессии генов изучали методом полимеразной цепной реакции в режиме реального времени. Результаты. Выявлен дифференциальный профиль экспрессии шести (RAD50, HMGN2, RBPJ, PABPC4, BRAP и DEK) из девяти исследуемых генов в различных гистологических типах опухолей молочной железы. Корреляции между изменениями в уровне экспрессии генов и наличием иммунного ответа против соответствующих антигенов не обнаружено. Выводы. Гены RAD50, HMGN2, RBPJ, PABPC4, BRAP и DEK антигенов МКМЖ, имеющих дифференциальный профиль экспрессии в различных гистологических типах опухолей молочной железы, являются потенциальными диагностическими маркерами рака молочной железы. Установлено, что изменение экспрессии исследованных генов не является обязательным условием возникновения иммунного ответа против их белковых продуктов. Ключевые слова: карцинома молочной железы, опухоль-ассоциированные антигены, иммунореактивность

Elucidating drivers of oral epithelial dysplasia formation and malignant transformation to cancer using RNAseq

Oral squamous cell carcinoma (OSCC) is a prevalent cancer with poor prognosis. Most OSCC progresses via a non-malignant stage called dysplasia. Effective treatment of dysplasia prior to potential malignant transformation is an unmet clinical need. To identify markers of early disease, we performed RNA sequencing of 19 matched HPV negative patient trios: normal oral mucosa, dysplasia and associated OSCC. We performed differential gene expression, principal component and correlated gene network analysis using these data. We found differences in the immune cell signatures present at different disease stages and were able to distinguish early events in pathogenesis, such as upregulation of many HOX genes, from later events, such as down-regulation of adherens junctions. We herein highlight novel coding and non-coding candidates for involvement in oral dysplasia development and malignant transformation, and speculate on how our findings may guide further translational research into the treatment of oral dysplasia

Tracking the antibody immunome in sporadic colorectal cancer by using antigen self-assembled protein arrays

© 2021 by the authors.Sporadic Colorectal Cancer (sCRC) is the third leading cause of cancer death in the Western world, and the sCRC patients presenting with synchronic metastasis have the poorest prognosis. Genetic alterations accumulated in sCRC tumor cells translate into mutated proteins and/or abnormal protein expression levels, which contribute to the development of sCRC. Then, the tumor-associated proteins (TAAs) might induce the production of auto-antibodies (aAb) via humoral immune response. Here, Nucleic Acid Programmable Protein Arrays (NAPPArray) are employed to identify aAb in plasma samples from a set of 50 sCRC patients compared to seven healthy donors. Our goal was to establish a systematic workflow based on NAPPArray to define differential aAb profiles between healthy individuals and sCRC patients as well as between non-metastatic (n = 38) and metastatic (n = 12) sCRC, in order to gain insight into the role of the humoral immune system in controlling the development and progression of sCRC. Our results showed aAb profile based on 141 TAA including TAAs associated with biological cellular processes altered in genesis and progress of sCRC (e.g., FSCN1, VTI2 and RPS28) that discriminated healthy donors vs. sCRC patients. In addition, the potential capacity of discrimination (between non-metastatic vs. metastatic sCRC) of 7 TAAs (USP5, ML4, MARCKSL1, CKMT1B, HMOX2, VTI2, TP53) have been analyzed individually in an independent cohort of sCRC patients, where two of them (VTI2 and TP53) were validated (AUC ~75%). In turn, these findings provided novel insights into the immunome of sCRC, in combination with transcriptomics profiles and protein antigenicity characterizations, wich might lead to the identification of novel sCRC biomarkers that might be of clinical utility for early diagnosis of the tumor. These results explore the immunomic analysis as potent source for biomarkers with diagnostic and prognostic value in CRC. Additional prospective studies in larger series of patients are required to confirm the clinical utility of these novel sCRC immunomic biomarkers.We gratefully acknowledge financial support from the Spanish Health Institute Carlos III (ISCIII) for the grants: FIS PI14/01538, FIS PI17/01930 and CB16/12/00400. We also acknowledge Fondos FEDER (EU) “Una manera de hacer Europa” and Junta Castilla-León (COVID19 grant COV20EDU/00187). Fundación Solórzano FS/38-2017. The Proteomics Unit belongs to ProteoRed, PRB3-ISCIII, supported by grant PT17/0019/0023, of the PE I + D + I 2017-2020, funded by ISCIII and FEDER. CNPq-National Council for Scientific and Technological Development (Brazil) (306258/2019-6) and FAPERJ-Foundation for Research Support of Rio de Janeiro State for the financial support (E-26/201.670/2017 and 210.379/2018). M. González-González is supported by MINECOPTA2019-017870-I.A. Landeira-Viñuela is supported by VIII Centenario-USAL PhD Program. P.J.-V. is supported by JCYL PhD Program and scholarship JCYL-EDU/601/2020. P.D. and E.B. are supported by a JCYL-EDU/346/2013 Ph.D. scholarship

Histopathological correlates of the biological variation in primary melanomas

Primary cutaneous melanoma is a highly heterogeneous tumour. My hypothesis is that the histopathological heterogeneity reflects biological variation, which is likely to have prognostic and predictive significance. A histopathological review of 798 primary melanomas from the Leeds Melanoma Cohort Study was recorded using virtual pathology. The tumour blocks had previously been sampled using a tissue microarray needle, yielding a core from which RNA was extracted and assayed using Illumina® WG-DASL. This provided the opportunity to compare histopathological characteristics with gene expression data derived from consistently sampled regions. RandomSpot© was used to estimate the percentage of stroma (POS) within cored regions. Statistical analyses were performed using STATA v14.2. Inter- and intraobserver agreement were analysed and robust measures were retained. Histopathological characteristics were analysed with respect to germline BAP1 mutation status to assess whether they could predict germline BAP1 mutation status. BAP-like histopathology was not significantly associated with germline BAP1 mutation status (deleterious versus none, Fisher’s exact test, p=0.1). A personal history of mesothelioma (Fisher’s exact test, p=0.005), or a family history of meningioma (Fisher’s exact test, p=0.005) or BCC (Fisher’s exact test, p=0.02) was associated with deleterious, germline BAP1 mutations. Cancer history appeared to be a better indicator of germline BAP1 mutation status than BAP-like histopathology. Several histopathological factors were predictive of melanoma-specific survival, including the POS. The area under the curve increased by 3% when the POS and AJCC stage were combined in ROC curve analysis. The POS was an independent predictor of melanoma-specific survival (HR 0.99, 95% CI 0.98-0.99, Cox proportional hazards model, p=0.005), even adjusting for known prognostic factors. SDF1 gene expression was significantly associated with the POS and was independently protective for melanoma-specific death (HR 0.8, 95% CI 0.68-0.94, Cox proportional hazards model, p=0.005) in adjusted analyses. The POS and SDF1 could represent novel predictive and prognostic biomarkers

MAL2 and tumor protein D52 (TPD52) are frequently overexpressed in ovarian carcinoma, but differentially associated with histological subtype and patient outcome

Background: The four-transmembrane MAL2 protein is frequently overexpressed in breast carcinoma, and MAL2 overexpression is associated with gain of the corresponding locus at chromosome 8q24.12. Independent expression microarray studies predict MAL2 overexpression in ovarian carcinoma, but these had remained unconfirmed. MAL2 binds tumor protein D52 (TPD52), which is frequently overexpressed in ovarian carcinoma, but the clinical significance of MAL2 and TPD52 overexpression was unknown. Methods: Immunohistochemical analyses of MAL2 and TPD52 expression were performed using tissue microarray sections including benign, borderline and malignant epithelial ovarian tumours. Inmmunohistochemical staining intensity and distribution was assessed both visually and digitally. Results: MAL2 and TPD52 were significantly overexpressed in high-grade serous carcinomas compared with serous borderline tumours. MAL2 expression was highest in serous carcinomas relative to other histological subtypes, whereas TPD52 expression was highest in clear cell carcinomas. MAL2 expression was not related to patient survival, however high-level TPD52 staining was significantly associated with improved overall survival in patients with stage III serous ovarian carcinoma (log-rank test, p < 0.001; n = 124) and was an independent predictor of survival in the overall carcinoma cohort (hazard ratio (HR), 0.498; 95% confidence interval (CI), 0.34-0.728; p < 0.001; n = 221), and in serous carcinomas (HR, 0.440; 95% CI, 0.294-0.658; p < 0.001; n = 182). Conclusions: MAL2 is frequently overexpressed in ovarian carcinoma, and TPD52 overexpression is a favourable independent prognostic marker of potential value in the management of ovarian carcinoma patients.11 page(s

Histopathological correlates of the biological variation in primary melanomas

Primary cutaneous melanoma is a highly heterogeneous tumour. My hypothesis is that the histopathological heterogeneity reflects biological variation, which is likely to have prognostic and predictive significance. A histopathological review of 798 primary melanomas from the Leeds Melanoma Cohort Study was recorded using virtual pathology. The tumour blocks had previously been sampled using a tissue microarray needle, yielding a core from which RNA was extracted and assayed using Illumina® WG-DASL. This provided the opportunity to compare histopathological characteristics with gene expression data derived from consistently sampled regions. RandomSpot© was used to estimate the percentage of stroma (POS) within cored regions. Statistical analyses were performed using STATA v14.2. Inter- and intraobserver agreement were analysed and robust measures were retained. Histopathological characteristics were analysed with respect to germline BAP1 mutation status to assess whether they could predict germline BAP1 mutation status. BAP-like histopathology was not significantly associated with germline BAP1 mutation status (deleterious versus none, Fisher’s exact test, p=0.1). A personal history of mesothelioma (Fisher’s exact test, p=0.005), or a family history of meningioma (Fisher’s exact test, p=0.005) or BCC (Fisher’s exact test, p=0.02) was associated with deleterious, germline BAP1 mutations. Cancer history appeared to be a better indicator of germline BAP1 mutation status than BAP-like histopathology. Several histopathological factors were predictive of melanoma-specific survival, including the POS. The area under the curve increased by 3% when the POS and AJCC stage were combined in ROC curve analysis. The POS was an independent predictor of melanoma-specific survival (HR 0.99, 95% CI 0.98-0.99, Cox proportional hazards model, p=0.005), even adjusting for known prognostic factors. SDF1 gene expression was significantly associated with the POS and was independently protective for melanoma-specific death (HR 0.8, 95% CI 0.68-0.94, Cox proportional hazards model, p=0.005) in adjusted analyses. The POS and SDF1 could represent novel predictive and prognostic biomarkers

Perturbation of 3D nuclear architecture, epigenomic dysregulation and aging, and cannabinoid synaptopathy reconfigures conceptualization of cannabinoid pathophysiology: part 1–aging and epigenomics

Much recent attention has been directed toward the spatial organization of the cell nucleus and the manner in which three-dimensional topologically associated domains and transcription factories are epigenetically coordinated to precisely bring enhancers into close proximity with promoters to control gene expression. Twenty lines of evidence robustly implicate cannabinoid exposure with accelerated organismal and cellular aging. Aging has recently been shown to be caused by increased DNA breaks. These breaks rearrange and maldistribute the epigenomic machinery to weaken and reverse cellular differentiation, cause genome-wide DNA demethylation, reduce gene transcription, and lead to the inhibition of developmental pathways, which contribute to the progressive loss of function and chronic immune stimulation that characterize cellular aging. Both cell lineage-defining superenhancers and the superanchors that control them are weakened. Cannabis exposure phenocopies the elements of this process and reproduces DNA and chromatin breakages, reduces the DNA, RNA protein and histone synthesis, interferes with the epigenomic machinery controlling both DNA and histone modifications, induces general DNA hypomethylation, and epigenomically disrupts both the critical boundary elements and the cohesin motors that create chromatin loops. This pattern of widespread interference with developmental programs and relative cellular dedifferentiation (which is pro-oncogenic) is reinforced by cannabinoid impairment of intermediate metabolism (which locks in the stem cell-like hyper-replicative state) and cannabinoid immune stimulation (which perpetuates and increases aging and senescence programs, DNA damage, DNA hypomethylation, genomic instability, and oncogenesis), which together account for the diverse pattern of teratologic and carcinogenic outcomes reported in recent large epidemiologic studies in Europe, the USA, and elsewhere. It also accounts for the prominent aging phenotype observed clinically in long-term cannabis use disorder and the 20 characteristics of aging that it manifests. Increasing daily cannabis use, increasing use in pregnancy, and exponential dose-response effects heighten the epidemiologic and clinical urgency of these findings. Together, these findings indicate that cannabinoid genotoxicity and epigenotoxicity are prominent features of cannabis dependence and strongly indicate coordinated multiomics investigations of cannabinoid genome-epigenome-transcriptome-metabolome, chromatin conformation, and 3D nuclear architecture. Considering the well-established exponential dose-response relationships, the diversity of cannabinoids, and the multigenerational nature of the implications, great caution is warranted in community cannabinoid penetration