Hereditary cancer syndromes linked to oxidative phosphorylation insufficiency

A theory that can best explain the facts of a phenomenon is more likely to advance knowledge than a theory that is less able to explain the facts. Cancer is generally considered a genetic disease based on the somatic mutation theory (SMT) where mutations in proto-oncogenes and tumor suppressor genes cause dysregulated cell growth. Evidence is reviewed showing that the mitochondrial metabolic theory (MMT) can better account for the hallmarks of cancer than can the SMT. Proliferating cancer cells cannot survive or grow without carbons and nitrogen for the synthesis of metabolites and ATP (Adenosine Triphosphate). Glucose carbons are essential for metabolite synthesis through the glycolysis and pentose phosphate pathways while glutamine nitrogen and carbons are essential for the synthesis of nitrogen-containing metabolites and ATP through the glutaminolysis pathway. Glutamine-dependent mitochondrial substrate level phosphorylation becomes essential for ATP synthesis in cancer cells that over-express the glycolytic pyruvate kinase M2 isoform (PKM2), that have deficient OxPhos, and that can grow in either hypoxia (0.1% oxygen) or in cyanide. The simultaneous targeting of glucose and glutamine, while elevating levels of non-fermentable ketone bodies, offers a simple and parsimonious therapeutic strategy for managing most cancers.

The inter-relationships between respiratory rates, proton electrochemical gradients (ΔH+) and extra-mitochondrial adenine nucleotide phosphorylation potentials (ΔGp(out) are examined during oxidative and substrate-level phosphorylation by mitochondria from the brown-adipose tissue of cold-adapted guinea-pigs. In the absence of net ATP synthesis, ΔGp(out) is proportional to ΔH+-when the latter is varied from 230 mV to 190 mV, and is consistent with a stoichiometry of proton translocation for ATP synthesis ( H+/ATP) of 2.6. When there is a net production of ATP, ΔGp(out) falls below the level predicted from ΔH+. When ATP is generated by substrate-level phosphorylation, ΔGp(out) can be much greater than that predicted from ΔH+. In the absence of substrate-level phosphorylation, respiration is controlled by ΔH+, regardless of whether energy dissipation is varied by addition of proton translocators or by addition of extra-mitochondrial ATP-hydrolysing systems. In contrast, the rate of respiration coupled to substrate-level phosphorylation appears to be controlled by the internal adenine nucleotide phosphorylation potential ΔGp(in). The rate of ATP synthesis by oxidative phosphorylation is dependent in ΔGp(out). In the absence of net ATP synthesis, both oxidative and substrate-level phosphorylation can maintain a ΔGp(out) in excess of 580 mV (56 kJ/mol), while in the presence of sufficient proton translocator to achieve uncontrolled respiration, a ΔGp(out) of 500 mV (48 kJ/mol) can be maintained by oxidative phosphorylation. Under conditions designed to approximate to those pertaining in the brown adipocyte during non-shivering thermogenesis, oxidative phosphorylation alone appears to be adequate to maintain cellular ATP levels. It was not possible to confirm reports of a specific role which could be assigned to substrate-level phosphorylation in the regulation of energy-dissipation by these mitochondria.

Hereditary Cancer Syndrome Recognition and Testing: Beyond BRCA

Hereditary cancer syndromes are genetic conditions that increase an individual’s risk for multiple cancer types, often due to mutations that affect critical cellular processes such as DNA repair and cell cycle regulation. Skin cancers, including malignant melanoma (MM), basal cell carcinoma (BCC), squamous cell carcinoma (SCC), and related precancerous lesions may be underrecognized in some hereditary cancer syndromes, as suggested by underlying biological mechanisms and their underreporting in studies. In this narrative review, we examine the skin cancer risks associated with the most prevalent hereditary cancer syndromes, including Li-Fraumeni syndrome (LFS), Lynch syndrome (LS), hereditary breast and ovarian cancer syndrome (HBOC), ATM-associated hereditary cancer syndrome, CHEK2-associated hereditary cancer syndrome, BRIP1-associated cancer predisposition, and hereditary leiomyomatosis and renal cell carcinoma (HLRCC). This review consolidates existing evidence and suggests that mixed cancer syndromes, especially LFS, LS, and HBOC but also pathogenic ATM and CHEK2 variants may predispose individuals to skin cancers, warranting tailored screening and preventive measures. On the basis of emerging evidence, we recommend dermatologic evaluation and individualized UV protection strategies for patients with reviewed hereditary cancer syndromes to reduce skin cancer risk and enhance early detection.

Oncogenes and tumor suppressor genes play different roles in carcinogenesis and tumor progression. However, very little attention has been paid to compare their mutational and evolutionary patterns. As such, these two groups of genes are often mingled together in computational modeling and analysis. To bridge this gap, we examined the evolutionary profiles of 150 oncogenes and 102 tumor suppressor genes and their somatic mutations recorded in the COSMIC database. We found that these two groups of genes display distinct evolutionary and mutational patterns. In general, oncogenes are more conserved than tumor suppressor genes, as revealed by multiple-species comparisons. The stronger purifying selection on oncogenes is also reflected at positions harboring somatic missense mutations. Thus, somatic mutations disrupting oncogenes tend to have higher functional impact than those disrupting tumor suppressor genes. However, the mutational landscape of oncogenes is often dominated by one or very few hotspots, while multiple hotspots and frequent sporadic mutations are found in tumor suppressor genes. Furthermore, CpG hypermutations contribute to 58% of highly recurrent mutations in tumor suppressor genes, but only 4% to those in oncogenes. These patterns indicate that most random somatic mutations in oncogenes are also under stronger purifying selection as compared to those in tumor suppressor genes. However, once an advantageous mutation in an oncogene arises, it tends to increase the fitness significantly such that a hard sweep pursues, which eventually reduces the mutational diversity of the tumor. On the contrary, the relatively mild selection on tumor suppressor genes allows more neutral mutations to accumulate. When eventually the deactivation of both copies of a tumor suppressor gene triggers positive selection, the mutational diversity of the tumor has increased significantly. These distinct evolutionary and mutational patterns warrant independent modeling of oncogenes and tumor suppressor genes in studies that incorporate these features in the analysis, such as prediction of driver mutations or inference of evolutionary paths for cancers. Citation Format: Li Liu, Yung Chang, Jieping Ye, Sudhir Kumar. Distinct evolutionary and mutational patterns in oncogenes and tumor suppressor genes. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1923. doi:10.1158/1538-7445.AM2015-1923

IA18: Tumor suppressor gene silencing by somatic mutations and promoter methylation leads to genomic instability in head and neck squamous cell carcinoma

Mutant TP53 disrupts age-related accumulation patterns of somatic mutations in multiple cancer types

Lynch Syndrome: A Single Hereditary Cancer Syndrome or Multiple Syndromes Defined by Different Mismatch Repair Genes?

Molecular Epidemiology of AML: Association of Somatic Gene Mutations with Epidemiologic Exposures and Outcomes in the Mayo Clinic AML Epidemiology Cohort

It is well established that carcinoma-associated fibroblasts (CAFs) differ phenotypically from fibroblasts associated with normal tissue, but the mechanisms underlying these differences remain controversial. Because CAFs can be propagated in vitro for extended periods and still maintain their cancer promoting phenotype, it has been proposed that they might have acquired somatic genetic alterations analogous to those observed in malignant epithelium. Whereas some investigators have reported frequent and profound genomic alterations in CAFs, other groups have found no such evidence. One striking common trait of those studies reporting frequent clonal somatic alterations in CAFs is the use of tissues and techniques which are well known to be highly prone to generating artefacts, such as limiting and poor quality DNA followed by highly multiplexed PCR-based analysis. We conclude that reported frequent clonal somatic mutations in CAFs are likely to be artefacts and are not the biological basis of the cancer promoting attributes of CAFs. [corrected]

Hereditary cancer syndromes, which are characterized by onset at an early age and an increased risk of developing certain tumors, are caused by germline pathogenic variants in tumor suppressor genes and are mostly inherited in an autosomal dominant manner. Therefore, hereditary cancer syndromes have been used as powerful models to identify and characterize susceptibility genes associated with cancer. Furthermore, clarification of the association between genotypes and phenotypes in one disease has provided insights into the etiology of other seemingly different diseases. Molecular genetic discoveries from the study of hereditary cancer syndrome have not only changed the methods of diagnosis and management, but have also shed light on the molecular regulatory pathways that are important in the development and treatment of sporadic tumors. The main cancer susceptibility syndromes that involve gynecologic cancers include hereditary breast and ovarian cancer syndrome as well as Lynch syndrome. However, in addition to these two hereditary cancer syndromes, there are several other hereditary syndromes associated with gynecologic cancers. In the present review, we provide an overview of the clinical features, and discuss the molecular genetics, of four rare hereditary gynecological cancer syndromes; Cowden syndrome, Peutz-Jeghers syndrome, DICER1 syndrome and rhabdoid tumor predisposition syndrome 2.

Non-small-cell lung cancers (NSCLCs) are largely classified into lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC), which have different therapeutic options according to its molecular profiles and immune checkpoint expression, especially PD-L1, which is a suppressive factor in the tumor microenvironment. The tumor microenvironment can be altered by the genomic mutations on specific innate immune genes as well as tumor suppressor genes, so it is essential to comprehend the association between tumor microenvironment and tumor suppressor genes to discover the promising immunotherapeutic strategy to overcome the resistance of immune check point blockade. In this study, we aimed to analyze how the somatic mutations in tumor suppressor genes affect the tumor immune microenvironment through a comprehensive analysis of mutational profiling on the representative tumor suppressor genes (TP53, CDKN2A, PTEN, RB1, BRCA1, BRCA2) and immune gene expression in The Cancer Genome Atlas (TCGA) 155 lung squamous cell carcinoma (LUSC) and 196 lung adenocarcinoma (LUAD) samples. Several microenvironmental factors, such as the infiltrating immune and stromal cells, were suppressed by the mutated tumor suppressor genes in LUSC, unlike in the LUAD samples. In particular, infiltrating immune cells such as macrophage, neutrophil, and dendritic cells were significantly reduced in tumors with mutated tumor suppressor genes’ group. In addition, the gene expressions for interleukin production and lymphocyte differentiation and PGC, C7, HGF, PLA2G2A, IL1RL1, CCR2, ALOX15B, CXCL11, FCN3 were significantly down-regulated, which were key immune genes for the cross-talk between LUSC microenvironment and tumor suppressors. Therefore, we generated evidence that TSG mutations in LUSC have an impact on tumor immune microenvironment, which suggests that TSG non-mutated patients will have the more inflamed tumors and are more likely to respond to immune checkpoint blockade therapy.

Renal cell carcinoma (RCC) affects nearly 300,000 people worldwide each year and is responsible for over 100,000 deaths each year. RCC is not a single disease; it is made up of a number of different types of cancer, with different histologies and clinical courses, responding differently to therapy and caused by different genes. There are currently 17 genes known to cause RCC, 14 of which are associated with inherited forms of the disease. Study of the RCC gene pathways has shown that RCC is fundamentally a metabolic disease. Much of what is known about the genetic basis of RCC has been learned from studying RCC-predisposition families. von Hippel-Lindau (VHL) is a hereditary cancer syndrome in which affected individuals are at risk for the development of tumors in a number of organs, including the kidneys. Patients affected with VHL are at risk for the development of bilateral, multifocal, clear cell renal cell carcinoma. Genetic linkage analysis in VHL families was performed to identify the VHL gene on the short arm of chromosome 3. VHL gene mutation that segregates with the disease is identified in 100% of VHL families. VHL gene mutation or methylation is also found in a high percentage of tumors from patients with sporadic, nonfamilial clear cell RCC. The product of the VHL gene, pVHL, has been found to form a complex with elongin C, elongin B, Cul2, and RBX1 to target the hypoxia-induced factors, HIF1/2, for oxygen-dependent ubiquitin-mediated degradation. Although 9 targeted therapeutic agents have been approved by the FDA for the treatment of patients with advanced RCC, many patients eventually progress and may succumb to this disease. High-grade, high-stage, low-survival clear cell RCC has been shown to be characterized by a pattern consistent with aerobic glycolysis, reduced oxidative phosphorylation, and a dependence on the pentose phosphate shunt. Clinical trials targeting the metabolic basis of clear cell RCC, including targeting HIF2 transcription, are currently under way. Hereditary papillary renal cell carcinoma (HPRC) is a hereditary cancer syndrome in which affected individuals are at risk for the development of bilateral, multifocal type 1 papillary RCC. HPRC is characterized by germline mutation of the MET proto-oncogene. MET gene alteration or amplification is found in a high percentage of tumors from patients with nonhereditary, sporadic Type 1 papillary renal cell carcinoma (PRCC). Clinical trials are currently under way targeting the MET pathway in patients with Type 1 PRCC. Birt-Hogg-Dubé is an inherited form of chromophobe RCC (ChRCC) in which affected individuals are at risk for the development of bilateral multifocal chromophobe and hybrid oncocytic RCC. Genetic linkage analysis identified the FLCN as the Birt-Hogg-Dubé gene. The product of the FLCN gene, folliculin, forms a complex with the FLCN binding proteins, FNIP1/2, and the gamma subunit of AMPK. Inactivation of the FLCN has been shown to result in activation of mTORC1/mTORC2. A clinical trial is currently being conducted to evaluate the effect of targeting the mTORC1 pathway in patients with Birt-Hogg-Dubé-associated renal tumors. Hereditary leiomyomatosis and renal cell carcinoma (HLRCC) is a hereditary cancer syndrome in which affected individuals are at risk for the development of cutaneous and uterine leiomyomas and an aggressive form of Type 2 PRCC. HLRCC is characterized by mutation of the gene for the Krebs cycle enzyme, fumarate hydratase (FH). HLRCC-associated type 2 PRCC has been shown to be characterized by a Warburg shift to aerobic glycolysis with decreased oxidative phosphorylation and a glutamine-dependent reductive carboxylation. Clinical trials are currently under way evaluating the effect of agents targeting the FH pathway in patients with HLRCC-associated RCC. SDH-RCC is an inherited from of renal cell carcinoma that occurs in families with germline mutation of succinate dehydrogenase (SDH) B,C, or D genes. Similar to FH-deficient RCC, SDH-RCC is characterized by a metabolic shift to aerobic glycolysis, significantly impaired oxidative phosphorylation (consistent with complex 2 dysfunction), and a glutamine-dependent reductive carboxylation. SDH-RCC renal tumors are malignant and have a propensity to spread when they are small. Understanding the metabolic basis of renal cell carcinoma has the potential to provide the foundation for the development of more effective forms of therapy for patients with these cancers.

Hereditary cancer syndromes (HCS) are genetic diseases with an increased risk of developing cancer. This research describes the implementation of a cancer prevention model, genetic counseling, and germline variants testing in an oncologic center in Mexico. A total of 315 patients received genetic counseling, genetic testing was offered, and 205 individuals were tested for HCS. In 6 years, 131 (63.90%) probands and 74 (36.09%) relatives were tested. Among the probands, we found that 85 (63.9%) had at least one germline variant. We identified founder mutations in BRCA1 and a novel variant in APC that led to the creation of an in-house detection process for the whole family. The most frequent syndrome was hereditary breast and ovarian cancer syndrome (HBOC) (41 cases with BRCA1 germline variants in most of the cases), followed by eight cases of hereditary non-polyposic cancer syndrome (HNPCC or Lynch syndrome) (with MLH1 as the primarily responsible gene), and other high cancer risk syndromes. Genetic counseling in HCS is still a global challenge. Multigene panels are an essential tool to detect the variants frequency. Our program has a high detection rate of probands with HCS and pathogenic variants (40%), compared with other reports that detect 10% in other populations.

Prostate Cancer (PCa) is a genetic disease that is characterized by multiple genomic alterations. Studies have shown that there is increasing associations between DNA repair genes and PCa. Previously we have reported somatic mutations in Polb and Polk enzymes that are critical for base excision repair and translesion DNA synthesis respectively. In the present study we identified frequently mutated genes that are involved in DNA repair pathway by sequencing all exons of DNA repair pathway genes (129). A total of 57 tumors with matched non tumor tissue was used. Tumors include 24 Caucasians, 21 African Americans (AA). PCa tumors that were ≥6 gleason score and ≥50% of viable tumor cells were only included. All the PCa were procured from Tulane University (TU) Hospital, New Orleans and ethical approvals were obtained from the TU Local Research Ethical Committee. Genomic DNA from tumors was using agilent SureSelect kit was customized to enrich the target that contained all exons of 129 genes of DNA repair pathways. Samples were sent for sequencing by Illumina HiSeq 2000. We validated experimentally somatic mutations in genes that were either affected by somatic non-synonymous or synonymous mutations with a frequency significantly greater than background rates (P<0.05). We considered a somatic mutation to be validated if the targeted sequencing confirmed the presence of the mutation in tumor and it was not found in the matched normal sample. Overall we identified 875 somatic mutations in AA, in which 414 were non-synonymous, 427 synonymous, 14 were stop-gain and 1 was frameshift mutation. AA demonstrated 52 somatic mutations/tumor and Caucasians exhibited 46 somatic mutations/tumor. In terms of Nucleotide excision repair (NER), Mismatch repair (MMR) and Base excision repair (BER) we identified variation in NER, MMR and BER pathways in AA [highest mutation in NER (mean-66) followed by MMR (mean-47) and then BER pathways (mean-37)] whereas our report shows that MMR, BER and NER equally mutated in Caucasians. Furthermore analysis of distribution of mutations between low grade (6) and high-grade Gleason scores (8 or >8) in AA and Caucasians revealed that 12 mutations per tumor for Gleason score 6, versus 22.3 mutations for Gleason 8, 9 or 10. Due to the limitation of samples with gleason score 6 in both races we could not draw a trend individually. Analysis of mutation spectra across the DNA repair genes revealed that C> T transitions (27%) markedly higher in AA PCa followed by T > C transitions (24%). Interestingly in Caucasians PCa C > T transitions (26.8%) were higher including marked increase of C > A (17%) and T > G (17%) transversions. Understanding the mutational changes at the individual patient level could enable personalized treatment and patient selection based on tumor mutational profile for clinical drug testing might be critical for development of new treatments strategies. Support PC094628, and NIH grant 8 P20 GM103518 Citation Format: Santosh Yadav, Muralidharan Anbalagan, Melody Baddoo, Erik Flemington, Krzysztof Moroz, Kathleen Hering-Smith, Nick Makridakis. Landscape of somatic mutations in DNA repair genes in prostate cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2753.