The PI3K/Akt Pathway in Tumors of Endocrine Tissues

The phosphatidylinositol 3-kinase (PI3K)/Akt pathway is a key driver in carcinogenesis. Defects in this pathway in human cancer syndromes such as Cowden’s disease and Multiple Endocrine Neoplasia result in tumors of endocrine tissues, highlighting its importance in these cancer types. This review explores the growing evidence from multiple animal and in vitro models and from analysis of human tumors for the involvement of this pathway in the following: thyroid carcinoma subtypes, parathyroid carcinoma, pituitary tumors, adrenocortical carcinoma, phaeochromocytoma, neuroblastoma, and gastroenteropancreatic neuroendocrine tumors. While data are not always consistent, immunohistochemistry performed on human tumor tissue has been used alongside other techniques to demonstrate Akt overactivation. We review active Akt as a potential prognostic marker and the PI3K pathway as a therapeutic target in endocrine neoplasia

Revisiting Epidermal Growth Factor Receptor (EGFR) Amplification as a Target for Anti-EGFR Therapy: Analysis of Cell-Free Circulating Tumor DNA in Patients With Advanced Malignancies.

PurposeTo date, evidence for tissue epidermal growth factor receptor (EGFR) overexpression as a biomarker for anti-EGFR therapies has been weak. We investigated the genomic landscape of EGFR amplification in blood-derived cell-free tumor DNA (cfDNA) across diverse cancers and the role of anti-EGFR therapies in achieving response.MethodsWe assessed EGFR amplification status among 28,584 patients with malignancies evaluated by clinical-grade next-generation sequencing (NGS) of blood-derived cfDNA (54- to 73-gene panel). Furthermore, we curated the clinical characteristics of 1,434 patients at the University of California San Diego who had cfDNA testing by this NGS test.ResultsOverall, EGFR amplification was detected in cfDNA from 8.5% of patients (2,423 of 28,584), most commonly in colorectal (16.3% [458 of 2,807]), non-small-cell lung (9.0% [1,096 of 12,197]), and genitourinary cancers (8.1% [170 of 2,104]). Most patients had genomic coalterations (96.9% [95 of 98]), frequently involving genes affecting other tyrosine kinases (72.4% [71 of 98]), mitogen-activated protein kinase cascades (56.1% [55 of 98]), cell-cycle-associated signals (52.0% [51 of 98]), and the phosphoinositide 3-kinase pathway (35.7% [35 of 98]). EGFR amplification emerged in serial cfDNA after various anticancer therapies (n = 6), including checkpoint inhibitors (n = 4), suggesting a possible role for these amplifications in acquired resistance. Nine evaluable patients with EGFR amplification were treated with anti-EGFR-based regimens; five (55.6%) achieved partial responses, including three patients whose tissue NGS lacked EGFR amplification.ConclusionEGFR amplification was detected in cfDNA among 8.5% of 28,584 diverse cancers. Most patients had coexisting alterations. Responses were observed in five of nine patients who received EGFR inhibitors. Incorporating EGFR inhibitors into the treatment regimens of patients harboring EGFR amplification in cfDNA merits additional study

The diverse molecular profiles of lynch syndrome-associated colorectal cancers are (highly) dependent on underlying germline mismatch repair mutations

Lynch syndrome (LS) is a hereditary cancer syndrome that accounts for 3% of all new colorectal cancer (CRC) cases. Patients carry a germline pathogenic variant in one of the mismatch repair (MMR) genes (MLH1, MSH2, MSH6 or PMS2), which encode proteins involved in a post-replicative proofreading and editing mechanism. The clinical presentation of LS is highly heterogeneous, showing high variability in age at onset and penetrance of cancer, which may be partly attributable to the molecular profiles of carcinomas. This review discusses the frequency of alterations in the WNT/B-CATENIN, RAF/MEK/ERK and PI3K/PTEN/AKT pathways identified in all four LS subgroups and how these changes may relate to the 'three pathway model' of carcinogenesis, in which LS CRCs develop from MMR-proficient adenomas, MMR-deficient adenomas or directly from MMR-deficient crypts. Understanding the specific differences in carcinogenesis for each LS subgroup will aid in the further optimization of guidelines for diagnosis, surveillance and treatment.Molecular tumour pathology - and tumour geneticsMTG2 - Moleculaire genetica van gastrointestinale tumore

Wnt and vitamin D at the crossroads in solid cancer

The Wnt/β-catenin signaling pathway is aberrantly activated in most colorectal cancers and less frequently in a variety of other solid neoplasias. Many epidemiological and experimental studies and some clinical trials suggest an anticancer action of vitamin D, mainly against colorectal cancer. The aim of this review was to analyze the literature supporting the interference of Wnt/β-catenin signaling by the active vitamin D metabolite 1α,25-dihydroxyvitamin D3. We discuss the molecular mechanisms of this antagonism in colorectal cancer and other cancer types. Additionally, we summarize the available data indicating a reciprocal inhibition of vitamin D action by the activated Wnt/β-catenin pathway. Thus, a complex mutual antagonism between Wnt/β-catenin signaling and the vitamin D system seems to be at the root of many solid cancers. Abnormal activation of the Wnt/β-catenin pathway is common in many types of solid cancers. Likewise, a large proportion of cancer patients have vitamin D deficiency. In line with these observations, Wnt/β-catenin signaling and 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3), the active vitamin D metabolite, usually have opposite effects on cancer cell proliferation and phenotype. In recent years, an increasing number of studies performed in a variety of cancer types have revealed a complex crosstalk between Wnt/β-catenin signaling and 1,25(OH)2D3. Here we review the mechanisms by which 1,25(OH)2D3 inhibits Wnt/β-catenin signaling and, conversely, how the activated Wnt/β-catenin pathway may abrogate vitamin D action. The available data suggest that interaction between Wnt/β-catenin signaling and the vitamin D system is at the crossroads in solid cancers and may have therapeutic applications.The work in the authors’ laboratory is funded by the Agencia Estatal de Investigación (PID2019-104867RB-I00/AEI/10.13039/501100011033), the Agencia Estatal de Investigación—Fondo Europeo de Desarrollo Regional (SAF2016-76377-R, MINECO/AEI/FEDER, EU), the Ministerio de Economía y Competitividad (SAF2017-90604-REDT/NuRCaMeIn), and the Instituto de Salud Carlos III—Fondo Europeo de Desarrollo Regional (CIBERONC; CB16/12/00273

Evaluation of dormancy states in cancer and associated therapeutic opportunities

Tumour mass dormancy and cancer cell quiescence represent the two facets of cancer dormancy and play key roles in cancer development and progression. Quiescence describes the reversible, proliferative arrest of individual cancer cells that has been observed as a contributing factor of resistance to chemotherapy and other treatments targeting cycling cells. In contrast, tumour mass dormancy describes the state of no net tumour growth, which can arise due to inadequate tumour vascularisation or anti- tumour immune response, during which tumours can acquire additional mutations and establish a microenvironment permissive for growth. Currently, both dormancy states remain poorly characterised. This thesis presents computational frameworks for evaluating the two states and comprehensively profiles their abundance and associated genomic and cellular features across 31 solid cancers from the Cancer Genome Atlas. Using machine learning approaches, I demonstrate that cancer cell quiescence preferentially arises in less mutated tumours with intact TP53 and DNA damage repair pathways. I also highlight novel genomic dependencies, such as CEP89 amplification, which drive an impairment of quiescence. Similarly, mutations within CASP8 and HRAS oncogenes are shown to be enriched and positively selected in samples with tumour mass dormancy. I also highlight an association between APOBEC mutagenesis and both dormancy states. Moreover, tumour mass dormancy is shown to be associated with infiltration with macrophages and cytotoxic and regulatory T cells but a decreased infiltration with Th17 cells. Lastly, using single-cell data, I demonstrate that quiescence underlies resistance to a wide range of therapies, including treatments targeting cell cycle regulation, proliferative kinase signalling and epigenetic regulation. Ultimately, this analysis sheds light on the underlying biology of cancer dormancy states, potentially highlighting vulnerabilities that can be targeted in the clinic. It also provides a transcriptional signature of therapy-tolerant quiescent cells that could be explored further in the clinic to monitor patient therapy response

The LKB1-SIK pathway: dysregulation in melanomagenesis and regulated use in skin cancer prevention

The presence of dark melanin (eumelanin) within human epidermis represents one of the strongest predictors of skin cancer risk. Topical rescue of eumelanin synthesis, previously achieved in “redhaired” Mc1r-deficient mice, demonstrated significant protection against UV damage and skin carcinogenesis. However, application of a topical strategy for human skin pigmentation has not been achieved, largely due to the greater barrier function of human epidermis. Salt Inducible Kinase (SIK) has been demonstrated to regulate MITF, the master regulator of pigment gene expression, through its effects on CREB regulated transcription coactivator (CRTC) and CRE binding protein (CREB) activity. Here, we describe the development of small molecule SIK inhibitors that were optimized for human skin penetration, resulting in MITF upregulation and induction of melanogenesis. When topically applied, pigment production was induced in Mc1r-deficient mice and normal human skin. These findings are the first to demonstrate a realistic pathway towards UV-independent topical modulation of human skin pigmentation, potentially impacting UV protection and skin cancer risk. Although MITF normally functions as a regulator of pigmentation, if amplified MITF can serve as a melanoma oncogene shown to cooperate with BRAF (V600E) to induce tumorigenic transformation of melanocytes . Only 10% of melanomas carry an MITF amplification emphasizing the need to identify pathways that modulate MITF expression . Liver kinase B1 (LKB1) regulates many cancer-relevant cell phenotypes and is a known SIK inducer . However, the interaction of the LKB1-SIK pathway and MITF in melanoma formation is not fully understood. Overall 49% of human melanomas in The Cancer Genome Atlas contain aberrations in LKB1, SIK1, SIK2, SIK3, CRTC1, CRTC2, CRTC3, or MITF . Here, we report that the LKB1-SIK axis can negatively regulate MITF expression, and our data suggests this is through increasing CRTC2 cytoplasmic localization. Rescue of LKB1 in LKB1-null G361 melanoma cells suppresses cell proliferation. MAP kinase pathway activation suppresses MITF, and knockdown of all three SIK isoforms rescues MITF expression in NRAS (Q61R) expressing melanocytes. Overall, our findings establish SIK and LKB1 as regulators of the CRTC-CREB-MITF pathway and through this regulation, potentially play a critical role as tumor suppressors in melanoma oncogenesis

Leveraging big data resources and data integration in biology: applying computational systems analyses and machine learning to gain insights into the biology of cancers

Recently, many "molecular profiling" projects have yielded vast amounts of genetic, epigenetic, transcription, protein expression, metabolic and drug response data for cancerous tumours, healthy tissues, and cell lines. We aim to facilitate a multi-scale understanding of these high-dimensional biological data and the complexity of the relationships between the different data types taken from human tumours. Further, we intend to identify molecular disease subtypes of various cancers, uncover the subtype-specific drug targets and identify sets of therapeutic molecules that could potentially be used to inhibit these targets. We collected data from over 20 publicly available resources. We then leverage integrative computational systems analyses, network analyses and machine learning, to gain insights into the pathophysiology of pancreatic cancer and 32 other human cancer types. Here, we uncover aberrations in multiple cell signalling and metabolic pathways that implicate regulatory kinases and the Warburg effect as the likely drivers of the distinct molecular signatures of three established pancreatic cancer subtypes. Then, we apply an integrative clustering method to four different types of molecular data to reveal that pancreatic tumours can be segregated into two distinct subtypes. We define sets of proteins, mRNAs, miRNAs and DNA methylation patterns that could serve as biomarkers to accurately differentiate between the two pancreatic cancer subtypes. Then we confirm the biological relevance of the identified biomarkers by showing that these can be used together with pattern-recognition algorithms to infer the drug sensitivity of pancreatic cancer cell lines accurately. Further, we evaluate the alterations of metabolic pathway genes across 32 human cancers. We find that while alterations of metabolic genes are pervasive across all human cancers, the extent of these gene alterations varies between them. Based on these gene alterations, we define two distinct cancer supertypes that tend to be associated with different clinical outcomes and show that these supertypes are likely to respond differently to anticancer drugs. Overall, we show that the time has already arrived where we can leverage available data resources to potentially elicit more precise and personalised cancer therapies that would yield better clinical outcomes at a much lower cost than is currently being achieved

The oncogenic role of histone chaperone ASF1 proteins in solid tumors

Chromatin is the essential medium connecting regulatory signals such as transcription factors and signaling pathways to the alteration of gene activity and cellular phenotypes. Aberrant chromatin (epigenetic) environment plays an important role in carcinogenesis. The fundamental unit of chromatin is the nucleosome which is composed of a histone core wrapped with 145-147 base pairs of DNA around. In the last decades, great efforts have been made to delineate the role of aberrant DNA methylation and chromatin/histone-remodeling factors in oncogenesis. However, recent evidence has merged that the dysregulation of histone chaperones also acts as a cancer-driver. Anti-silencing function 1 (ASF1) is the most conserved histone H3-H4 chaperone, regulating histone metabolism. ASF1 proteins include two paralogs ASF1A and ASF1B in mammals. ASF1A and ASF1B have been reported as oncogenes in human cancers. Data from the Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) databases show that ASF1A and ASF1B are overexpressed in 20 and 24 different types of cancers, respectively. Thus, in this thesis, I explored the oncogenic role of histone chaperone ASF1 and underlying molecular mechanisms in several solid tumors. In Paper I, the role for ASF1A in gastrointestinal cancer (GIC) was investigated. We discovered that ASF1A interacted with the oncogenic transcription factor β-catenin and promoted the transcription of β-catenin target genes (c-MYC, cyclin D1, ZEB1 and LGR5). The increased expression of these genes stimulated proliferation, stemness and migration/invasion of GIC cells. Over-expression and knockdown of ASF1A boosts and inhibits in vivo tumor growth and/or metastasis in mouse models, respectively. Higher levels of ASF1A expression predict significantly shorter patient survival in colorectal cancer (CRC). Further analyses of the Gene Expression Omnibus dataset validate higher ASF1A expression predicting a poor prognosis in CRC patients. Taken together, this study reveals the novel function of ASF1A as a transcription co-factor independent of its canonical role and the potential value of ASF1A for outcome prediction and targeted treatment in GIC. In Paper II, we show that ASF1A overexpression is widespread in human malignancies and is required for the infinite proliferation of cancer cells. When ASF1A was knocked-down in wild-type (wt) p53 carrying cells derived from hepatocellular carcinoma (HCC) and prostate cancer (PCa), DNA damage response was activated and up-regulation of p53-p21cip1 expression consequently occurred. These cells eventually underwent cellular senescence. Higher ASF1A expression and/or lower p21cip1 expression predicts a poor outcome in HCC patients. Thus, ASF1A may be a therapeutic target and a prognostic factor in HCC and other cancers. In Paper III, we evaluated whether ASF1B has diagnostic and prognostic values in adrenocortical carcinoma (ACC) and regulates invasion and metastasis. We first analyzed TCGA and GTEx data and found that the ASF1B gene was amplified in two thirds of ACC tumors and associated with its overexpression. ASF1B expression correlates with the ACC diagnostic criteria of the Weiss scoring system. Higher ASF1B expression and ASF1B copy number predict a poor outcome in the TCGA cohort of ACC patients. Knockdown of ASF1B in ACC cells impairs migration and invasion ability by inhibiting expression of the transcription factor FOXM1; whereas ASF1B over-expression exhibits opposing effects. These findings suggest that ASF1B may be a useful factor for ACC diagnostics and prognostication, and potentially a novel target for ACC therapy as well. Collectively, the results presented in this thesis gain profound insights into the oncogenic role of ASF1 in several solid tumors and demonstrated novel activities of ASF1 proteins beyond their conserved histone chaperone function. These findings will inspire further exploration of both the clinical and biological roles of ASF1 in precision oncology

ERBB4 mutations in cancer and amyotrophic lateral sclerosis

ErbB receptor tyrosine kinases, epidermal growth factor receptor (EGFR, also known as ErbB1), ErbB2 (HER2 or NEU), ErbB3 (HER3), and ErbB4 (HER4), transduce signals borne by extracellular ligands into central cellular responses such as proliferation, survival, differentiation, and apoptosis. Mutations in ERBB genes are frequently detected in human malignant diseases of epithelial and neural origin, making ErbB receptors important drug targets. Targeting EGFR and ErbB2 has been successful in eg. lung and breast cancer, respectively, and mutations in these genes can be used to select patients that are responsive to the targeted treatment. Although somatic ERBB4 mutations have been found in many high-incidence cancers such as melanoma, lung cancer, and colorectal cancer and germ-line ERBB4 mutations have been linked to neuronal disorders and cancer, ErbB4 has generally been neglected as a potential drug target. Thus, the consequences of ERBB4 mutations on ErbB4 biology are largely unknown. This thesis aimed to elucidate the functional consequences and assess the clinical significance of somatic and germ-line ERBB4 mutations in the context of cancer and amyotrophic lateral sclerosis. The results of this study indicated that cancer-associated ERBB4 mutations can promote aberrant ErbB4 function by activating the receptor or inducing qualitative changes in ErbB4 signaling. ERBB4 mutations increased survival or decreased differentiation in vitro, suggesting that ERBB4 mutations can be oncogenic. Importantly, the potentially oncogenic mutations were located in various subdomains in ErbB4, possibly providing explanation for the characteristic scattered pattern of mutations in ERBB4. This study also demonstrated that hereditary variation in ERBB4 gene can have a significant effect on the prognosis of breast cancer. In addition, it was shown that hereditary or de novo germ-line ERBB4 mutations that predispose to amyotrophic lateral sclerosis inhibit ErbB4 activity. Together, these results suggest that ErbB4 should be considered as a novel drug target in cancer and amyotrophic lateral sclerosis.ERBB4-geenin mutaatiot syövässä ja amyotrofisessa lateraaliskleroosissa ErbB reseptorit, epidermaalisen kasvutekijän reseptori (EGFR tai ErbB1), ErbB2 (HER2 tai NEU), ErbB3 (HER3) ja ErbB4 (HER4), välittävät solun ulkopuolisten kasvutekijöiden tuomia signaaleja solun sisään, ja siten säätelevät keskeisiä solun toimintoja kuten kasvua, selviytymistä, erilaistumista ja kuolemaa. ERBB-geenien mutaatioita havaitaan toistuvasti eri syövissä. ErbB-reseptorit ovat merkittäviä lääkehoidon kohdemolekyylejä. Mutatoituneisiin EGFR- ja ErbB2-reseptoreihin kohdistettuja lääkehoitoja käytetään mm. keuhko- ja rintasyöpäpotilaiden hoidossa. Somaattisia ERBB4-geenin mutaatioita on havaittu useissa yleisissä syövissä kuten melanoomassa, keuhkosyövässä sekä paksu- ja peräsuolisyövässä. ERBB4-geenistä on tunnistettu myös monia ituradan mukana periytyviä mutaatioita keskushermoston sairauksissa ja syövissä. ErbB4-reseptorin merkitys lääkehoidon kohteena tunnetaan kuitenkin huonosti. Tässä tutkimuksessa pyrittiin selvittämään, miten ERBB4-geenin mutaatiot vaikuttavat reseptorin toimintaan, sekä arvioimaan ERBB4-geenin mutaatioiden kliinistä merkitystä syövässä ja amyotrofisessa lateraaliskleroosissa. Tutkimuksen tulokset osoittavat, että syövässä esiintyvät ERBB4 geenin mutaatiot voivat johtaa epänormaaliin reseptorin toimintaan joko aktivoimalla reseptorin, tai aiheuttamalla muutoksia reseptorin solunsisäisessä viestinvälityksessä. Nämä muutokset johtivat lisääntyneeseen syöpäsolujen selviytymiseen tai vähentyneeseen solujen erilaistumiseen in vitro. Tulosten perusteella ErbB4-reseptorin mutaatiot voivat olla onkogeenisiä. Huomionarvoista on, että nämä mahdollisesti onkogeeniset mutaatiot olivat jakaantuneet useaan ErbB4-reseptorin rakenteelliseen alayksiköön. Tutkimuksessa osoitetiin myös, että ERBB4-geenin perinnöllinen variaatio voi vaikuttaa rintasyöpäpotilaan taudin ennusteeseen. Lisäksi tutkimuksessa näytettiin, että ERBB4 geenin joko perinnölliset tai de novo ituradan mutaatiot, jotka altistavat amyotrofiselle lateraaliskleroosille, vähentävät ErbB4-reseptorin aktiivisuutta. Tulosten perusteella mutatoitunut ErbB4-reseptori voi olla potentiaalinen lääkehoidon kohde syövässä ja amyotrofisessaSiirretty Doriast