A probabilistic method for leveraging functional annotations to enhance estimation of the temporal order of pathway mutations during carcinogenesis

Abstract Background Cancer arises through accumulation of somatically acquired genetic mutations. An important question is to delineate the temporal order of somatic mutations during carcinogenesis, which contributes to better understanding of cancer biology and facilitates identification of new therapeutic targets. Although a number of statistical and computational methods have been proposed to estimate the temporal order of mutations, they do not account for the differences in the functional impacts of mutations and thus are likely to be obscured by the presence of passenger mutations that do not contribute to cancer progression. In addition, many methods infer the order of mutations at the gene level, which have limited power due to the low mutation rate in most genes. Results In this paper, we develop a Probabilistic Approach for estimating the Temporal Order of Pathway mutations by leveraging functional Annotations of mutations (PATOPA). PATOPA infers the order of mutations at the pathway level, wherein it uses a probabilistic method to characterize the likelihood of mutational events from different pathways occurring in a certain order. The functional impact of each mutation is incorporated to weigh more on a mutation that is more integral to tumor development. A maximum likelihood method is used to estimate parameters and infer the probability of one pathway being mutated prior to another. Simulation studies and analysis of whole exome sequencing data from The Cancer Genome Atlas (TCGA) demonstrate that PATOPA is able to accurately estimate the temporal order of pathway mutations and provides new biological insights on carcinogenesis of colorectal and lung cancers. Conclusions PATOPA provides a useful tool to estimate temporal order of mutations at the pathway level while leveraging functional annotations of mutations.

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Intratumoral Adipocyte-High Breast Cancer Enrich for Metastatic and Inflammation-Related Pathways but Associated with Less Cancer Cell Proliferation

International Journal of Molecular Sciences ◽

10.3390/ijms21165744 ◽

2020 ◽

Vol 21 (16) ◽

pp. 5744 ◽

Cited By ~ 8

Author(s):

Yoshihisa Tokumaru ◽

Masanori Oshi ◽

Eriko Katsuta ◽

Li Yan ◽

Jing Li Huang ◽

...

Keyword(s):

Breast Cancer ◽

Cell Proliferation ◽

Cancer Progression ◽

Cancer Biology ◽

The Cancer Genome Atlas ◽

Related Gene ◽

Immune Microenvironment ◽

Gene Sets ◽

Tumor Immune Microenvironment ◽

Er Positive

Cancer-associated adipocytes are known to cause inflammation, leading to cancer progression and metastasis. The clinicopathological and transcriptomic data from 2256 patients with breast cancer were obtained based on three cohorts: The Cancer Genome Atlas (TCGA), GSE25066, and a study by Yau et al. For the current study, we defined the adipocyte, which is calculated by utilizing a computational algorithm, xCell, as “intratumoral adipocyte”. These intratumoral adipocytes appropriately reflected mature adipocytes in a bulk tumor. The amount of intratumoral adipocytes demonstrated no relationship with survival. Intratumoral adipocyte-high tumors significantly enriched for metastasis and inflammation-related gene sets and are associated with a favorable tumor immune microenvironment, especially in the ER+/HER2- subtype. On the other hand, intratumoral adipocyte-low tumors significantly enriched for cell cycle and cell proliferation-related gene sets. Correspondingly, intratumoral adipocyte-low tumors are associated with advanced pathological grades and inversely correlated with MKI67 expression. In conclusion, a high amount of intratumoral adipocytes in breast cancer was associated with inflammation, metastatic pathways, cancer stemness, and favorable tumor immune microenvironment. However, a low amount of adipocytes was associated with a highly proliferative tumor in ER-positive breast cancer. This cancer biology may explain the reason why patient survival did not differ by the amount of adipocytes.

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Biological mechanisms linked to inflammation in cancer: Discovery of tumor microenvironment-related biomarkers and their clinical application in solid tumors

The International Journal of Biological Markers ◽

10.1177/1724600820906155 ◽

2020 ◽

Vol 35 (1_suppl) ◽

pp. 8-11 ◽

Cited By ~ 3

Author(s):

Paola Nisticò ◽

Gennaro Ciliberto

Keyword(s):

Tumor Microenvironment ◽

Tumor Cells ◽

Cancer Progression ◽

Cancer Biology ◽

Tumor Development ◽

Short Paper ◽

Great Relevance ◽

Cellular Components ◽

The Relationship

Our view of cancer biology radically shifted from a “cancer-cell-centric” vision to a view of cancer as an organ disease. The concept that genetic and/or epigenetic alterations, at the basis of cancerogenesis, are the main if not the exclusive drivers of cancer development and the principal targets of therapy, has now evolved to include the tumor microenvironment in which tumor cells can grow, proliferate, survive, and metastasize only within a favorable environment. The interplay between cancer cells and the non-cellular and cellular components of the tumor microenvironment plays a fundamental role in tumor development and evolution both at the primary site and at the level of metastasis. The shape of the tumor cells and tumor mass is the resultant of several contrasting forces either pro-tumoral or anti-tumoral which have at the level of the tumor microenvironment their battle field. This crucial role of tumor microenvironment composition in cancer progression also dictates whether immunotherapy with immune checkpoint inhibitor antibodies is going to be efficacious. Hence, tumor microenvironment deconvolution has become of great relevance in order to identify biomarkers predictive of efficacy of immunotherapy. In this short paper we will briefly review the relationship between inflammation and cancer, and will summarize in 10 short points the key concepts learned so far and the open challenges to be solved.

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MLL-Rearranged Acute Myeloid Leukemias Drive Expression Of Mir-9, a Critical Oncogene In Leukemogenesis

Blood ◽

10.1182/blood.v122.21.3740.3740 ◽

2013 ◽

Vol 122 (21) ◽

pp. 3740-3740

Author(s):

Colles Price ◽

Ping Chen ◽

Zejuan Li ◽

Yuanyuan Li ◽

Anissa Wiley ◽

...

Keyword(s):

Messenger Rna ◽

Cancer Biology ◽

Conflicts Of Interest ◽

Univariate Analysis ◽

The United States ◽

The Cancer Genome Atlas ◽

Leukemic Cells ◽

Sequencing Data ◽

Significant Difference ◽

Acute Myeloid

Abstract A critical area of cancer biology is the study of the deregulation of noncoding RNAs called microRNAs (miRNAs). Acute leukemia represents one of the most deadly cancers in the United States. One subset of leukemia with a poor to intermediate clinical outcome are chromosomal translocations involving Mixed Lineage Leukemia (MLL). As MLL-translocations are sufficient to drive leukemogenesis, and few additional mutations are observed in patients, it is imperative to understand the biology driving leukemogenesis. Previously, we and others have shown that several miRNAs are deregulated in MLL-rearranged Acute Myeloid Leukemia (AML). To identify miRNAs that are driving leukemogenesis we performed messenger RNA and miRNA expression profiling on primary patient samples and identified microRNA-9 (miR-9) as specifically overexpressed in MLL-rearranged AML. We further confirmed this observation using publically available microRNA sequencing data from the Cancer Genome Atlas (TCGA) and several AML cell lines. After showing that MLL directly binds and regulates miR-9 we show that depletion of MLL-fusion expression leads to the loss of miR-9 expression. Using publically available Illumina 450K methylation data from TCGA, we show that there is no significant difference in modified cytosine between miR-9 high and miR-9-low patients, suggesting that expression of miR-9 is likely not be regulated by DNA methylation machinery in AML patients. We show that miR-9 in the presence of MLL-AF9 (a common MLL-fusion) promotes colony growth over multiple passages while blocking miR-9 using a miR-9 sponge remarkably inhibits MLL-fusion-mediated cell transformation. Furthermore, we show that miR-9 increases proliferation and reduces apoptosis of human MLL-rearranged leukemic cells in vitro using MTT and Caspase 3/7 assays. We then show that co-transfection of miR-9 with MLL-AF9 in a bone marrow transplantation assay results in a higher leukemia burden in vivo compared to MLL-AF9 alone and promotes an immature cellular phenotype. Using microarray data we found several putative miR-9 targets by identifying genes that had an inverse correlation to miR-9. Next, we verified several genes were being inhibited by miR-9 such as Ras homology gene family member H (RHOH) and Ring1- and YY1-binding protein (RYBP). To understand the role of miR-9 in context with other miRNAs we did an association analysis of the top 300 differentially expressed miRNAs in the TCGA dataset. We found interestingly, that two of the miR-9 genes, miR-9-1 and miR-9-2, are highly correlated with each other across all the patients although they are located on distinct chromosomes. We also found that several other miRs were either negatively (e.g., miR-130a and miR-221) or positively (e.g., miR-191 and miR-642) associated with miR-9 expression, suggesting that these miRs might be operating either cooperatively or antagonistically in a complex circuitry. To support this hypothesis we found in univariate analysis that miR-9 itself was not a good predictor of patient survival but was a better predictor when combined with other miRs including the miR-181 family. Together this suggests that miR-9 is an important and critical regulator of MLL-rearranged AML and is a very good candidate for potential therapeutic targeting. Disclosures: No relevant conflicts of interest to declare.

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Role of the Hsp90-Immunophilin Heterocomplex in Cancer Biology

Current Cancer Therapy Reviews ◽

10.2174/1573394715666190102120801 ◽

2020 ◽

Vol 16 (1) ◽

pp. 19-28

Author(s):

Sonia A. De Leo ◽

Nadia R. Zgajnar ◽

Gisela I. Mazaira ◽

Alejandra G. Erlejman ◽

Mario D. Galigniana

Keyword(s):

Cancer Progression ◽

Cancer Biology ◽

Steroid Receptors ◽

Human Cancer ◽

Tumor Development ◽

Biological Properties ◽

Tetratricopeptide Repeats ◽

Cellular Processes ◽

Client Factors ◽

Cancer Tissues

The identification of new factors that may function as cancer markers and become eventual pharmacologic targets is a challenge that may influence the management of tumor development and management. Recent discoveries connecting Hsp90-binding immunophilins with the regulation of signalling events that can modulate cancer progression transform this family of proteins in potential unconventional factors that may impact on the screening and diagnosis of malignant diseases. Immunophilins are molecular chaperones that group a family of intracellular receptors for immunosuppressive compounds. A subfamily of the immunophilin family is characterized by showing structural tetratricopeptide repeats, protein domains that are able to interact with the C-terminal end of the molecular chaperone Hsp90, and via the proper Hsp90-immunophilin complex, the biological properties of a number of client-proteins involved in cancer biology are modulated. Recent discoveries have demonstrated that two of the most studied members of this Hsp90- binding subfamily of immunophilins, FKBP51 and FKBP52, participate in several cellular processes such as apoptosis, carcinogenesis progression, and chemoresistance. While the expression levels of some members of the immunophilin family are affected in both cancer cell lines and human cancer tissues compared to normal samples, novel regulatory mechanisms have emerged during the last few years for several client-factors of immunophilins that are major players in cancer development and progression, among them steroid receptors, the transctiption factor NF-κB and the catalytic subunit of telomerase, hTERT. In this review, recent findings related to the biological properties of both iconic Hsp90-binding immunophilins, FKBP51 and FKBP52, are reviewed within the context of their interactions with those chaperoned client-factors. The potential roles of both immunophilins as potential cancer biomarkers and non-conventional pharmacologic targets for cancer treatment are discussed.

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Early and multiple origins of metastatic lineages within primary tumors

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1525677113 ◽

2016 ◽

Vol 113 (8) ◽

pp. 2140-2145 ◽

Cited By ~ 84

Author(s):

Zi-Ming Zhao ◽

Bixiao Zhao ◽

Yalai Bai ◽

Atila Iamarino ◽

Stephen G. Gaffney ◽

...

Keyword(s):

Cancer Progression ◽

Cancer Biology ◽

Tumor Development ◽

Evolutionary Process ◽

Driver Mutations ◽

Cancer Evolution ◽

Driver Genes ◽

Genetic Changes ◽

Primary Tumors ◽

Multiple Origins

Many aspects of the evolutionary process of tumorigenesis that are fundamental to cancer biology and targeted treatment have been challenging to reveal, such as the divergence times and genetic clonality of metastatic lineages. To address these challenges, we performed tumor phylogenetics using molecular evolutionary models, reconstructed ancestral states of somatic mutations, and inferred cancer chronograms to yield three conclusions. First, in contrast to a linear model of cancer progression, metastases can originate from divergent lineages within primary tumors. Evolved genetic changes in cancer lineages likely affect only the proclivity toward metastasis. Single genetic changes are unlikely to be necessary or sufficient for metastasis. Second, metastatic lineages can arise early in tumor development, sometimes long before diagnosis. The early genetic divergence of some metastatic lineages directs attention toward research on driver genes that are mutated early in cancer evolution. Last, the temporal order of occurrence of driver mutations can be inferred from phylogenetic analysis of cancer chronograms, guiding development of targeted therapeutics effective against primary tumors and metastases.

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A secondary role for hypoxia and HIF1 in the regulation of (IFNγ-induced) PD-L1 expression in melanoma

Cancer Immunology Immunotherapy ◽

10.1007/s00262-021-03007-1 ◽

2021 ◽

Author(s):

Anneloes van Duijn ◽

Karin J. Willemsen ◽

Nathalie O. P. van Uden ◽

Lieke Hoyng ◽

Sterre Erades ◽

...

Keyword(s):

Mrna Expression ◽

Immune Surveillance ◽

Tumor Development ◽

Human Melanoma ◽

The Cancer Genome Atlas ◽

Minor Role ◽

Sequencing Data ◽

Secondary Role ◽

A Minor ◽

Stat Pathway

AbstractCancer cells are able to escape immune surveillance by upregulating programmed death ligand 1 (PD-L1). A key regulator of PD-L1 expression is transcriptional stimulation by the IFNγ/JAK/STAT pathway. Recent studies suggest that hypoxia can induce PD-L1 expression. As hypoxia presents a hallmark of solid tumor development, hypoxic control of PD-L1 expression may affect the efficacy of cancer immunotherapy. This study aims to explore the hypoxic regulation of PD-L1 expression in human melanoma, and its interaction with IFNγ-induced PD-L1 expression. Analysis of the cutaneous melanoma dataset from the cancer genome atlas revealed a significant correlation of the HIF1-signaling geneset signature with PD-L1 mRNA expression. However, this correlation is less pronounced than other key pathways known to control PD-L1 expression, including the IFNγ/JAK/STAT pathway. This secondary role of HIF1 in PD-L1 regulation was confirmed by analyzing single-cell RNA-sequencing data of 33 human melanoma tissues. Interestingly, PD-L1 expression in these melanoma tissues was primarily found in macrophages. However, also in these cells STAT1, and not HIF1, displayed the most pronounced correlation with PD-L1 expression. Moreover, we observed that hypoxia differentially affects PD-L1 expression in human melanoma cell lines. Knockdown of HIF1 expression indicated a minor role for HIF1 in regulating PD-L1 expression. A more pronounced influence of hypoxia was found on IFNγ-induced PD-L1 mRNA expression, which is controlled at a 952 bp PD-L1 promoter fragment. These findings, showing the influence of hypoxia on IFNγ-induced PD-L1 expression, are relevant for immunotherapy, as both IFNγ and hypoxia are frequently present in the tumor microenvironment.

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The Pancreatic Microbiome is Associated with Carcinogenesis and Worse Prognosis in Males and Smokers

Cancers ◽

10.3390/cancers12092672 ◽

2020 ◽

Vol 12 (9) ◽

pp. 2672

Author(s):

Jaideep Chakladar ◽

Selena Z. Kuo ◽

Grant Castaneda ◽

Wei Tse Li ◽

Aditi Gnanasekar ◽

...

Keyword(s):

Cancer Progression ◽

Immune Suppression ◽

Large Scale ◽

The Cancer Genome Atlas ◽

Human Pancreatic Cancer ◽

Sequencing Data ◽

Cancer Genome Atlas ◽

And Gender ◽

Worse Prognosis ◽

Genome Atlas

An intra-pancreatic microbiota was recently discovered in several prominent studies. Since pancreatic adenocarcinoma (PAAD) is one of the most lethal cancers worldwide, and the intratumor microbiome was found to be a significant contributor to carcinogenesis in other cancers, this study aims to characterize the PAAD microbiome and elucidate how it may be associated with PAAD prognosis. We further explored the association between the intra-pancreatic microbiome and smoking and gender, which are both risk factors for PAAD. RNA-sequencing data from The Cancer Genome Atlas (TCGA) were used to infer microbial abundance, which was correlated to clinical variables and to cancer and immune-associated gene expression, to determine how microbes may contribute to cancer progression. We discovered that the presence of several bacteria species within PAAD tumors is linked to metastasis and immune suppression. This is the first large-scale study to report microbiome-immune correlations in human pancreatic cancer samples. Furthermore, we found that the increased prevalence and poorer prognosis of PAAD in males and smokers are linked to the presence of potentially cancer-promoting or immune-inhibiting microbes. Further study into the roles of these microbes in PAAD is imperative for understanding how a pro-tumor microenvironment may be treated to limit cancer progression.

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The Liver Microbiome Is Implicated in Cancer Prognosis and Modulated by Alcohol and Hepatitis B

Cancers ◽

10.3390/cancers12061642 ◽

2020 ◽

Vol 12 (6) ◽

pp. 1642

Author(s):

Jaideep Chakladar ◽

Lindsay M. Wong ◽

Selena Z. Kuo ◽

Wei Tse Li ◽

Michael Andrew Yu ◽

...

Keyword(s):

Hepatitis B ◽

Cancer Progression ◽

Suppressive Effect ◽

The Cancer Genome Atlas ◽

Cancer Prognosis ◽

Microbial Abundance ◽

Sequencing Data ◽

Etiological Factors ◽

Induced Tumors ◽

Tumor Suppressive Effect

Hepatocellular carcinoma (HCC) is one of the deadliest cancers in the world. Previous studies have identified the importance of alcohol and hepatitis B (HBV) infection on HCC carcinogenesis, indicating synergy in the methods by which these etiologies advance cancer. However, the specific molecular mechanism behind alcohol and HBV-mediated carcinogenesis remains unknown. Because the microbiome is emerging as a potentially important regulator of cancer development, this study aims to classify the effects of HBV and alcohol on the intratumoral liver microbiome. RNA-sequencing data from The Cancer Genome Atlas (TCGA) were used to infer microbial abundance. This abundance was then correlated to clinical variables and to cancer and immune-associated gene expression, in order to determine how microbial abundance may contribute to differing cancer progression between etiologies. We discovered that the liver microbiome is likely oncogenic after exposure to alcohol or HBV, although these etiological factors could decrease the abundance of a few oncogenic microbes, which would lead to a tumor suppressive effect. In HBV-induced tumors, this tumor suppressive effect was inferred based on the downregulation of microbes that induce cancer and stem cell pathways. Alcohol-induced tumors were observed to have distinct microbial profiles from HBV-induced tumors, and different microbes are clinically relevant in each cohort, suggesting that the effects of the liver microbiome may be different in response to different etiological factors. Collectively, our data suggest that HBV and alcohol operate within a normally oncogenic microbiome to promote tumor development, but are also able to downregulate certain oncogenic microbes. Insight into why these microbes are downregulated following exposure to HBV or alcohol, and why the majority of oncogenic microbes are not downregulated, may be critical for understanding whether a pro-tumor liver microbiome could be suppressed or reversed to limit cancer progression.

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CloneSig: Joint inference of intra-tumor heterogeneity and signature deconvolution in tumor bulk sequencing data

10.1101/825778 ◽

2019 ◽

Cited By ~ 2

Author(s):

Judith Abécassis ◽

Fabien Reyal ◽

Jean-Philippe Vert

Keyword(s):

Cancer Progression ◽

Tumor Heterogeneity ◽

Cancer Genomics ◽

Computational Method ◽

The Cancer Genome Atlas ◽

Sequencing Data ◽

Joint Inference ◽

Nucleotide Context ◽

Cancer Genome Atlas ◽

Mutational Processes

The possibility to sequence DNA in cancer samples has triggered much effort recently to identify the forces at the genomic level that shape tumorigenesis and cancer progression. It has resulted in novel understanding or clarification of two important aspects of cancer genomics: (i) intra-tumor heterogeneity (ITH), as captured by the variability in observed prevalences of somatic mutations within a tumor, and (ii) mutational processes, as revealed by the distribution of the types of somatic mutation and their immediate nucleotide context. These two aspects are not independent from each other, as different mutational processes can be involved in different subclones, but current computational approaches to study them largely ignore this dependency. In particular, sequential methods that first estimate subclones and then analyze the mutational processes active in each clone can easily miss changes in mutational processes if the clonal decomposition step fails, and conversely information regarding mutational signatures is overlooked during the subclonal reconstruction. To address current limitations, we present CloneSig, a new computational method to jointly infer ITH and mutational processes in a tumor from bulk-sequencing data, including whole-exome sequencing (WES) data, by leveraging their dependency. We show through an extensive benchmark on simulated samples that CloneSig is always as good as or better than state-of-the-art methods for ITH inference and detection of mutational processes. We then apply CloneSig to a large cohort of 8,954 tumors with WES data from the cancer genome atlas (TCGA), where we obtain results coherent with previous studies on whole-genome sequencing (WGS) data, as well as new promising findings. This validates the applicability of CloneSig to WES data, paving the way to its use in a clinical setting where WES is increasingly deployed nowadays.

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Extracellular Matrix Characterization in Gastric Cancer Helps to Predict Prognosis and Chemotherapy Response

Frontiers in Oncology ◽

10.3389/fonc.2021.753330 ◽

2021 ◽

Vol 11 ◽

Author(s):

Zhi Yang ◽

Feifei Xue ◽

Minhuan Li ◽

Xingya Zhu ◽

Xiaofeng Lu ◽

...

Keyword(s):

Gastric Cancer ◽

Extracellular Matrix ◽

Cancer Progression ◽

Poor Prognosis ◽

The Cancer Genome Atlas ◽

P Value ◽

Chemotherapy Response ◽

Sequencing Data ◽

Systematic Analysis ◽

Canonical Pathways

The extracellular matrix (ECM) plays a central role in the formation of the tumor microenvironment. The deposition of the ECM is associated with poor prognosis in a variety of tumors. Aberrant ECM deposition could undermine the effect of chemotherapy and immunotherapy. However, there is no systematic analysis on the relationship between the ECM and prognosis or chemotherapy effect. In the present study, we applied the gene set variation analysis (GSVA) algorithm to score 2199 canonical pathways in 2125 cases of probe or sequencing data and identified the core matrisome as the driving factor in gastric cancer progression. We classified gastric cancer samples into three clusters according to the composition of the ECM and evaluated clinical and multi-omics characterization of ECM phenotypes. The ECM score was evaluated by GSVA score of core matrisome and a higher ECM score predicted poor prognosis of gastric cancer [Hazard Ratio (HR), 2.084; p-value < 2 × 10−16]. In The Cancer Genome Atlas (TCGA) cohort and KUGH, YUSH, and KUCM cohorts, we verified that patients with a low ECM score could benefit from chemotherapy. By contrast, patients with a high ECM score did not achieve satisfactory response from chemotherapy. Determining the characteristics of the ECM microenvironment might help to predict the prognosis and chemotherapy response of patients with gastric cancer, and help to resolve the enigma of chemoresistance acquisition, as well as providing inspiration to develop combination therapy.

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