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New Topoisomerase Inhibitors in Clinical Trials

Posted in Cancer and Current Therapeutics, CANCER BIOLOGY & Innovations in Cancer Therapy, Cell Biology, Drug Delivery Platform Technology, Pharmaceutical Analytics, Pharmaceutical Discovery, Pharmacologic toxicities, Small Molecules in Development of Therapeutic Drugs, tagged Cancer - General, Cell Biology, Clinical trial, DNA, DNA repair, FDA, Food and Drug Administration, medicine, research, topoisomerase on October 14, 2015| Leave a Comment »

New Topoisomerase Inhibitors in Clinical Trials

Curator: Stephen J. Williams, Ph.D.

Below is a great review of topoisomerase in cancer, approved inhibitors as well as some in clinical trials.

Biomolecules 2015, 5, 1652-1670; doi:10.3390/biom5031652

OPEN ACCESS

biomolecules

ISSN 2218-273X

www.mdpi.com/journal/biomolecules/

Review

Inhibition of Topoisomerase (DNA) I (TOP1): DNA Damage Repair and Anticancer Therapy

Yang Xu and Chengtao Her *

School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Mail Drop 64-7520, Pullman, WA 99164, USA; E-Mail: davidxy22@vetmed.wsu.edu

* Author to whom correspondence should be addressed; E-Mail: cher@wsu.edu; Tel.: +1-509-335-7537; Fax: +1-509-335-4159.

Academic Editors: Wolf-Dietrich Heyer, Thomas Helleday and Fumio Hanaoka Received: 22 May 2015 / Accepted: 14 July 2015 / Published: 22 July 2015

Abstract: Most chemotherapy regimens contain at least one DNA-damaging agent that preferentially affects the growth of cancer cells. This strategy takes advantage of the differences in cell proliferation between normal and cancer cells. Chemotherapeutic drugs are usually designed to target rapid-dividing cells because sustained proliferation is a common feature of cancer [1,2]. Rapid DNA replication is essential for highly proliferative cells, thus blocking of DNA replication will create numerous mutations and/or chromosome rearrangements—ultimately triggering cell death [3]. Along these lines, DNA topoisomerase inhibitors are of great interest because they help to maintain strand breaks generated by topoisomerases during replication. In this article, we discuss the characteristics of topoisomerase (DNA) I (TOP1) and its inhibitors, as well as the underlying DNA repair pathways and the use of TOP1 inhibitors in cancer therapy.

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Type IB Topoisomerases and Inhibitors
1.1. TOP1

DNA topoisomerases resolve topological constraints that may arise from DNA strand separation and are therefore important for transcription and replication [4]. There are six topoisomerases in humans, classified as Type IA, IB and IIA. Type IA topoisomerases TOP3a and TOP3b cleave one DNA strand to relax only negative supercoiling. In addition, TOP3a forms the BTR complex with BLM and RMI1/2, which plays a role in the dissolution of double-Holliday junctions [5]. Type IIA topoisomerases TOP2a and TOP2b generate double-strand breaks on one DNA molecule to allow the passing of other DNA strands [6]. Topoisomerases are attractive drug targets in cancer therapy. For example, the commonly used anticancer agents doxorubicin and etoposide (VP-16) are TOP2 inhibitors [7]. Type IB topoisomerases include the nuclear TOP1 and mitochondrial TOP1mt [4]. TOP1 initiates the DNA relaxation by nicking one DNA strand. It then forms a TOP1-DNA cleavage complex (TOP1cc) by covalently linked to the 3′-phosphate end via its tyrosine residue Y723 (3′-P-Y). Following the resolution of topological entanglements and the removal of TOP1, the 5′-hydroxyl end is realigned with the 3′-end for religation. Each nicking-closing cycle enables the relaxation of one DNA supercoiling (Figure 1).

Figure 1. A schematic representation of strand passages catalyzed by three types of topoisomerases (adapted from ref. [8]).

TOP1 is essential for embryonic development in mammals [9]. Although TOP1 plays an important role in the deconvolution of supercoils arising amid DNA replication, the precise steps involved with

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the recruitment of TOP1 to topological constraints remains to be revealed. It appears that in yeast TOP1 travels at a distance of 600 bp ahead of the replication fork [10] and remains associated with the GINS-MCM complex [11]. However, the yeast TOP1 is distinct from its human counterpart in that it has little effect on fork progression or the firing of replication origin [12]. In humans, TOP1 binds to the regions of the pre-replicative complex in cells during the M, early G1, and G1/S phases of the cell cycle to control the firing of replication origins [12]. This difference may explain why yeast cells are viable in the absence of TOP1. In addition, TOP1 also has functions in transcription that are independent of its role in resolving DNA topological entanglements. First, TOP1 is known to repress transcription by binding to TFIID [13]. Second, inhibition of TOP1 can cause the induction of c-Jun in leukemia cells, suggesting its additional role in the control of transcription [14]. Furthermore, TOP1 interacts with the splicing factor ASF/SF2 by which it promotes the maturation of RNA—through suppressing the formation of R-loops (RNA-DNA hybrids)—and prevents collision between transcription bubble and replication fork [15,16]. It appears that the levels of TOP1 have to be dynamically regulated. In B cells, TOP1 is reduced by activation-induced cytidine deaminase (AID) to facilitate class-switch recombination (CSR) and somatic hypermutation (SHM) [17,18]. Although TOP1mt is important for mitochondrial integrity and metabolism, mice lacking mitochondrial TOP1mt are viable and fertile but they are associated with increased negative supercoiling of mtDNA [19,20].

1.2. TOP1 Inhibitors

Stabilization of TOP1cc by topoisomerase poison is detrimental to cells due to the disruption of DNA uncoiling, increased strand breaks, and unstable RNA transcripts as well as incomplete DNA replication [21]. The TOP1 inhibitor camptothecin (CPT), first isolated from the Chinese tree Camptotheca acuminate, was clinically used for cancer treatment long before it was identified as a TOP1 inhibitor [22]. Due to side effects, CPT is no longer used clinically and it has been replaced by more effective and safer TOP1 inhibitors [23]. Currently, CPT derivatives topotecan (trade name: Hycamtin) and irinotecan (CPT-11, trade name: Camptosar) are routinely used to treat colorectal, ovarian and lung cancers, while a few other TOP1 inhibitors are being tested in clinical trials.

CPT is a 5-ring alkaloid that is active in its closed E-ring (lactone) form but it is inactive with an open E-ring (carboxylate) at physiological and alkaline pH [24]. Therefore, CPT is not effective for inhibiting TOP1mt due to a higher pH mitochondrial environment. The inactive form of CPT tends to bind to serum albumin, which might be a reason for its side effects. CPT is highly specific for TOP1 and the binding is of relatively low affinity and can be reversed after drug removal. These features make the action of CPT controllable [24], and in fact CPT is widely used in studies of replication-associated DNA damage response. There are a few CPT derivatives and non-CPT TOP1 inhibitors [4,8,24]. For example, CPT derivatives Diflomotecan and S39625 were designed to stabilize the E-ring. Irinotecan has the bis-piperidine side chain to increase its water solubility, but it also contributes to some side effects. Non-CPTs—such as indolocarbazoles, phenanthrolines (e.g., ARC-111) and indenoisoquinolines—refer to drugs that have no typical CPT E-ring structures but they can still specifically target TOP1 and bind irreversibly to TOP1cc. Some of the CPT derivatives (i.e., Gimatecan and Belotecan) and non-CPTs (i.e., NSC 725776 and NSC 724998) are presently tested in clinical trials [23].

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How does CPT trap TOP1cc? Analysis of the crystal structure and modeling suggest that CPT-TOP1-DNA forms a ternary complex to prevent the two DNA ends from religation [25–27]. Although it is still controversial on how CPT is intercalated into DNA, it seems that CPT traps TOP1cc with a thymine (T) at the -1 position and a guanine (G) at the +1 position on the scissile strand, and it is therefore sequence-specific [28]. Three amino acid residues of the TOP1 enzyme, R364, D533 and N722, combined with DNA bases, contribute to the stabilization of the ternary complex by forming hydrogen bonds and hydrophobic interactions. It is of note that several point mutations, including N722S, in Camptotheca acuminata TOP1 confer resistance to CPT [29]. Interestingly, the same amino acids also contribute to the inhibition of TOP1 by non-CPT drugs [24].

Repair of TOP1 Poison-Induced DNA Lesions

As aforementioned, CPT-induced trapping of TOP1cc creates a single strand break with a free 5′-hydroxyl group, whereas the 3′-phosphate is connected to Y723 of TOP1 (3′-P-Y). At least two pathways contribute to the repair of DNA lesions created by TOP1 poison [30]. The tyrosyl-DNA-phosphodiesterase (TDP1) pathway starts with the ubiquitination and proteasome-mediated degradation of TOP1 in the CPT-TOP1-DNA complex to generate a 3′-P end linked to a short peptide [31]. TDP1 then cleaves the P-Y bond to release the 3′-P end; however, the 3′-P end cannot be directly ligated to the 5′-OH end because of the requirements of DNA ligases. The human polynucleotide kinase (PNKP) can process the DNA ends by functioning as both a 3′-phosphatase and a kinase to generate the required 3′-OH and 5′-P termini for direct ligation. The rest of the repair events can be best described by the single-strand break (SSB) repair pathway, which will be discussed below. Indeed, TDP1 and PNKP are tightly associated with the SSB repair machinery [32,33].

The endonuclease pathway requires multiple endonucleases to excise the DNA—usually at a few nucleotides away from the 3′-P-TOP1 end – on the scissile strand to release the DNA-TOP1 complex [30]. Initial studies were carried out to identify genes that functioned in CPT repair in the absence of TDP1 in yeast [34,35]. These studies led to the identification of RAD1-RAD10, SLX1-SLX4, MUS81-MMS4, MRE11-SAE2 as well as genes involved in recombination. The RAD1-RAD10 (human XPF/ERCC4-ERCC1) complex is a DNA structure-specific endonuclease that can act on 5′ overhang structures [36]. Interestingly, the cleavage site of XPF-ERCC1 is in the non-protruding DNA strand, about 3–4 nucleotides away from the 3′ end [36]. Therefore, trapped TOP1ccs can be removed by this endonuclease activity. Likewise, MUS81-MMS4 (human MUS81-EME1) can also cleave nicked duplex at the 5′ of the nick [37]. The SLX1-SLX4 endonuclease, although not tested on nicked duplexes, is able to process 3′ flap and other DNA structures [38,39]. In human cells, SLX4 also associates with XPF-ERCC1 and MUS81-EME1 endonucleases to process specific DNA intermediates [39,40]. Moreover, MRE11-RAD50 cleaves the 3′-P-Y bond and resects DNA to produce a 3′-OH end [41]. A direct role of SAE2 (human CtIP) in processing 3′-P-TOP1 is unknown, and its endonuclease activity appears to be limited to the 5′ flap or DNA “hairpin” structures [42,43]. Nonetheless, the endonuclease activity of CtIP is essential for processing CPT adducts [42]. In addition, like CtIP, the 5′ flap endonuclease RAD27 (human FEN1) seems to be unable to directly process 3′-P-TOP1 ends [44]. However, the gap endonuclease activity of FEN1 is important for processing stalled replication forks and CPT-induced adducts [45]. The role of FEN1 in SSB repair will be discussed further in the next section.

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During DNA replication, SSBs created by CPT are most likely converted to double-strand breaks (DSBs) by replication fork runoff. This conversion appears to be dependent on the proteolysis of TOP1 [46]. The repair of one-ended DSBs, as will be discussed in the next section, is largely dependent on homologous recombination (HR). However, low doses of CPT may also induce PARP1 and/or RAD51 dependent replication fork regression—generating no or few DSBs [47,48]. The regressed fork leads to the formation of a “chicken foot” DNA structure by newly synthesized strands [3,49,50]. The formation of regressed fork can be largely suppressed by ATR, EXO1, and DNA2 [51–53]. However, fork reversal can also be beneficial as it provides time for the repair of TOP1-induced DNA lesions by TDP1, thereby preventing DSB formation and the activation of error-prone non-homologous end-joining (NHEJ) [30].

Pathways Involved in the Repair of CPT-Induced DNA Lesions

Normal cells use DNA damage response (DDR) pathways to maintain genomic stability [54]. As aforementioned, SSB and DSB repair mechanisms are the two major DDR pathways that repair TOP1-induced DNA lesions. Paradoxically, cancer cells exploit DDR pathways to accumulate necessary genomic alterations for promoting proliferation. Furthermore, altered DDR and apoptotic responses in cancer cells are the major obstacles to successful chemotherapy. Thus, the delineation of TOP1-related SSB and DSB repair mechanisms is of great importance for identifying drug targets that can selectively affect cancer cell survival.

3.1. Single-Strand Break (SSB) Repair

Trapping of TOP1cc results in a 3′-P-TOP1 end and a 5′-OH terminus. Because the two ends cannot be directly religated, the persisting SSB is likely to be detected by PARP1 in which activated PARP1 catalyzes the synthesis of poly(ADP-ribose) (PAR) chains for recruiting repair proteins [55]. This reaction can be rapidly reversed by PARG, which hydrolyzes the PAR chains. The PAR chains at the SSB sites are important for the recruitment of XRCC1 that functions as a loading dock for other SSB repair proteins including TDP1 and PNKP. TDP1 generates 3′-P and PNKP converts 3′-P to 3′-OH, and PNKP also converts 5′-OH to 5′-P, making ends compatible for religation with no base loss. The rejoining of the 3′-OH and 5′-P ends is mainly mediated by LIG3, in which XRCC1 mediates the recruitment of LIG3.

If the trapped TOP1cc intermediates are processed by endonucleases, the initial SSBs will be converted to 3′-OH and 5′-OH ends with a gap over a few nucleotides (in the case of XPF-ERCC1, the loss is in the range of 3–4 nt), leading to the activation of PARP1 and XRCC1 recruitment. Consequentially, Pol3 recruited by XRCC1 can catalyze the gap filling, and PCNA-Polö/E also plays a role in this process [55]. If the 5′-OH is not processed by PNKP, the 5′-flap resulted from gap filling is likely to be removed by FEN1, which explains why FEN1 deficiency also leads to an increased CPT sensitivity. The final ligation is catalyzed by LIG1 because of the presence of PCNA.

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3.2. Double-Strand Break (DSB) Repair

Successful DSB repair requires concerted actions of proteins involved in DNA damage signaling and repair [54]. To repair TOP1 poison-induced DNA lesions, ATR signaling is required due to the runoff of replication fork and the presence of long single-strand DNA (ssDNA) [56]. The full activation of ATR follows a “two-man” rule—the ssDNA-ATRIP-dependent recruitment of ATR kinase and the RAD17 clamp loader/9-1-1/TOPBP1 mediator loading at the ssDNA-dsDNA junction. ATR phosphorylates CHEK1 to harness cell cycle arrest. If one-ended DSB is formed, ATM will be activated through the action of the MRE11-RAD50-NBS1 (MRN) complex. ATM mainly phosphorylates CHEK2 to mediate cell cycle arrest. Both ATM and ATR are able to phosphorylate hundreds of proteins in response to DSB formation [57]. One remarkable substrate is the histone H2AX, which can be phosphorylated by both kinases to yield g-H2AX. It is conceived that the propagation of g-H2AX signaling along the chromatin facilitates MDC1 recruitment and BRCA1 signaling via the MDC1-RNF8-RNF168-RAP80 ubiquitin cascade—events that are essential for HR [58].

The repair of TOP1 poison-induced DNA lesions is in essence the repair of one-ended DSBs, which facilitates the restoration of replication forks to restart DNA replication. It is important to note that one-ended DSB repair occurs in the S phase and relies on HR rather than NHEJ [59]. The first step in HR is end resection to generate a 3′-overhang for homology searching. A TOP1 cleavage in the leading strand may require end resection by the MRN-CtIP-BRCA1 and BLM-EXO1-DNA2 complexes [60], whereas a cleavage in the lagging strand automatically forms a 3′-overhang. Rad51 then associates with the 3′-ssDNA to form a nucleofilament for strand invasion, which leads to the formation of a D-loop structure [61]. This process continues with DNA synthesis, branch migration and the resolution of Holliday junction structures to reconstitute a functional replication fork [62]. TOP1 poisons can also lead to the formation of two-ended DSB if two replication forks collide into each other at the site of SSB. The repair of this type of DSBs is not aimed for fork restoration and can be accomplished by the classical DSB repair mechanisms [61].

3.3. Genes Involved in CPT-Induced Damage Repair

A long list of genes, in which mutations confer sensitivity to CPT in yeast, chicken or mammalian cells, has been compiled [24,30,63]. With no surprise, many genes involved in SSB and DSB repair are on the list, such as PARP1, XRCC1, PNKP, TDP1 for SSB repair; MRN, ATM-CHK2, ATR-CHK1 for DSB signaling; BRCA1/2, XRCC2, XRCC3 for HR. Most recently, the hMSH5-FANCJ complex has also been implicated to play a role in CPT-induced DNA damage response and repair [64]. Mutations in the binding partners of these repair factors are also likely to sensitize cells to CPT treatment. For example, depletion of the MRN-binding partner hnRNPUL increases the sensitivity to CPT [65]; and deficiencies in ZRANB3 and SPIDR, binding partners of PCNA and RAD51, cause CPT hypersensitivity in cancer cells [66–68]. In addition, the two DNA helicases BLM and WRN have also been implicated in the repair of CPT-induced DNA lesions [69,70]. Early studies revealed that chicken BLM knockout cells and human BLM-deficient fibroblasts showed increased sensitivity to CPT [71,72]. On the contrary, mouse BLM knockout embryonic stem cells showed mild resistance to

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CPT [73]. This discrepancy is likely attributable to the complexity of CPT-induced DNA lesion repair as well as different treatment conditions and experimental systems.

Interstrand crosslinks (ICLs) resemble CPT-induced lesions in that they block both replication and transcription [74]. They may induce replication fork reversal and fork collapse, which require DNA incision for lesion processing and HR for repair. ICL repair is accomplished by the coordinated actions of 17 Fanconi anemia (FA) genes whose mutations contribute to FA in patients [75]. Depletion of FANCP/SLX4 or FANCQ/XPF causes cellular sensitivity to CPT because they form an endonuclease complex involved in the repair of trapped TOP1cc [38]. Likewise, depletion of FANCS/BRCA1, FANCD1/BRCA2, FANCN/PALB2 or FANCO/RAD51C sensitizes cells to CPT because of their involvement in HR [76]. Accordingly, depletion of the FA core complex except FANCM—involved in fork reversal—is not expected to increase CPT sensitivity because they are unable to recognize the trapped TOP1cc [76]. However, the roles of FANCI, D2, J and FAN1 in the process are elusive due to conflicting reports presumably reflecting different experimental systems [76–78]. For example, in a multicolor competition assay, loss of FANCI or FAN1 rendered cells sensitive to CPT treatment [77]. However, this observation could not be recapitulated in studies performed with FANCI-deficient lymphoblasts and FAN1-depleted HEK293 cells [76,79], indicating that the involvement of these two genes in CTP sensitivity might be cell type specific.

It is interesting to note that the MMS22L-TONSL complex plays a prominent role in mediating CPT sensitivity [80–83]. Depletion of this complex impairs RAD51 foci formation and triggers G2/M arrest, indicating that the MMS22L-TONSL complex participates in HR repair. Furthermore, this complex associates with MCM, FACT, ASF1 and histones. FACT and ASF1 are histone chaperones that function in H2A/H2B and H3/H4 chromatin assembly and disassembly, respectively [84]. They recycle parental histones from old DNA strands unwound by MCM and incorporate them into newly synthesized DNA strands. FACT and ASF1 also function in checkpoint signaling; therefore the involvement of MMS22L-TONSL in CPT response implies the existence of a close association between HR, DNA damage signaling and replication restart.

TOP1 Inhibition in Cancer Treatment

The understanding of the function of TOP1 and the cellular effects of TOP1 inhibition has been a stepping-stone for the development of effective CPT derivatives in cancer therapy. Since TOP1 functions in normal and cancer cells, the use of low doses of TOP1 inhibitors are actively sought to treat cancers that heavily rely on the function of TOP1 for survival (e.g., highly malignant, rapid-dividing tumor cells). In fact, the FDA-approved CPT derivatives topotecan and irinotecan are currently used to treat ovarian and colorectal cancers, respectively [24].

Furthermore, the promising results from a Phase I trial have warranted further evaluation of the CPT derivative Diflomotecan in Phase II trials [85]. Other derivatives like Gimatecan, Lurtotecan and Exatecan are also being tested in clinical trials (Table 1). The non-CPT indolocarbazole BMS-250749 showed great anti-tumor activity against preclinical xenograft models [86], but no further evaluation beyond Phase I trials is presently available (Table 2). Another indolocarbazole compound Edotecarin has shown promising anti-tumor activity in xenograft models and it is now advanced to Phase II studies of patients with advanced solid tumors [87]. By contrast, Phenanthroline ARC-111 (topovale)

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was potently against human tumor xenografts and displayed anti-cancer activity in colon and Wilms’ tumors [88]; however, no result from Phase I clinical trials is available owing to profound bone marrow toxicity [89]. To date, indenoisoquinolines are the most promising non-CPT inhibitors in clinical trials. LMP400 (NSC 743400, indotecan) and LMP776 (NSC 725776, indimitecan) show significant anti-tumor activities in animal models and both are being evaluated in Phase I clinical trials for relapsed solid tumors and lymphomas [8,90].

Table 1. CPT derivatives in clinical trials [91].

Name Structure Clinical Trial Malignancy Reference

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Given the observation that CPT-mediated TOP1 inhibition provokes DNA repair activities, a synergistic effect is then anticipated on cancer cells by inhibition of TOP1 and downregulation of DNA repair activities. The rationale for this approach is to accelerate the accumulation of DNA breaks and trigger cellular apoptosis, probably through mitotic catastrophe [92]. Which DNA repair pathways can we exploit? Currently, the major interests are in SSB and DSB repair mechanisms. Indeed, PARP inhibitors can enhance the cytotoxicity of TOP1 inhibitors in cancer cell lines as well as in mouse models [93–96]. Phase I studies of combination therapy using PARP inhibitors veliparib or olaparib (FDA-approved) together with topotecan were carried out in patients with advanced solid tumors but showed some dose-dependent side effects [97,98]. TDP1 can be another potential target because it functions directly downstream of PARP1 in the repair of TOP1 poison-induced DNA lesions [99]. TDP1 inhibitors sensitize cells to CPT treatment in vitro [100,101], however in vivo evaluation is presently unavailable due to unsuitable properties of the compounds [102].

Table 2. Non-CPT derivatives in preclinical and clinical trials [91].

Name Structure Clinical Trial Malignancy Reference

Indolocarbazoles
(Edotecarin,
BMS-250749)

Phase II

(Edotecarin, Pfizer)

Stomach, breast
neoplasms

Preclinical
(BMS-250749)

Anti-tumor activity
in preclinical
xenograft models

[86,87,103]

Phenanthridines
(ARC-111/topovale)

Anti-tumor activity

Preclinical in preclinical [88,89,103]
xenograft models

Indenoisoquinolines
(LMP400, LMP776)

Phase I Lymphomas [8,90,103]

DSB repair can be targeted by either inhibition of DSB signaling or inhibition of HR. ATM and ATR inhibitors can largely increase the sensitivity to CPT in cancer cells [104,105]. This can be explained by the fact that abrogation of the cell cycle arrest will allow cells with unreplicated or unrepaired chromosomes to enter mitosis thereby triggering mitotic catastrophe and cell death. Similarly, CHEK1 and CHEK2 inhibitors are tested in Phase I studies in combination with irinotecan [106,107]. Inhibitors that can directly block HR proteins are very limited [108]. This is partially attributed to the fact that HR genes are often mutated in cancer cells, thus diminishing the enthusiasm for developing HR inhibitors. One diterpenoid compound, however, was found to be able to inhibit the function of BRCA1 and render cytotoxicity in human prostate cancer cells [109]. Several RAD51 inhibitors have also been

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identified but have not been tested in cell lines [110]. Inhibition of BRCA1 and RAD51 can be also achieved indirectly by harnessing corresponding kinases [106]. Clearly, defective hMRE11 sensitizes colon cancer cells to CPT treatment [111]. Although MRE11-deficeint tumor xenografts failed to display significant growth inhibition by irinotecan alone, combining thymidine with irinotecan caused a dramatic growth delay [112].

TOP1 inhibitors might be also useful for treating cancers with BRCA1/2 mutations. The successful use of PARP inhibitors in treating BRCA1/2-deficient tumors has ignited a broad interest in searching for synthetic lethality among DNA damage response and repair genes [113,114]. In the PARP-BRCA1/2 example, the accumulation of SSBs by PARP inhibition would lead to the formation of DSBs during replication. In HR-deficient cells, DSBs can only be repaired by illegitimate (toxic) NHEJ—joining one-ended DSBs from different locations—leading to cell death [115,116]. However, resistance to PARP inhibitors can arise in BRCA1-deficient tumors during treatment from either genetic reversion of BRCA1 mutations or the loss of NHEJ [117–122]. Therefore, it would be beneficial to explore the possibility of developing a similar synthetic lethal strategy to use TOP1 inhibitors in the treatment of BRCA1/2-deficient tumors.

Figure 2. An overview of the effects of TOP1 inhibition is provided. Inhibitors and key DNA repair factors are highlighted.

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Conclusions

Trapping of TOP1 by inhibitors generates SSBs and DSBs that are repaired by their corresponding repair pathways (Figure 2). Therefore, developing effective TOP1 inhibitors not only provides powerful tools to study DNA replication and repair but also establishes a foundation to devise new synthetic lethal strategies for efficient cancer treatments. The accumulation of DNA strand breaks (SSBs and DSBs) by TOP1 inhibition in HR-deficient tumor cells is expected to enhance cytotoxicity. However, increased DNA repair activities in cancer cells can make TOP1 inhibitors less effective, so silencing of repair pathways in conjunction with the use of TOP1 inhibitors offers an attractive new means for cancer control. Since each tumor is unique, it would be advantageous to identify the individualities of DNA repair pathways or biomarkers reflecting the changes of DNA repair activities in tumor cells [92,123]. This will make it possible to achieve better and predictable prognosis through tailored therapeutic regimens. Given that TOP1 is essential for transcription and DNA replication, future design of novel TOP1 inhibitors and combinational therapy strategies should aim to increase therapeutic efficacy of the inhibitors, thus reducing side effects.

Acknowledgments

The work in the Her laboratory is supported by the NIH grant GM084353.

Author Contributions

Yang Xu and Chengtao Her wrote and revised the article.

Conflicts of Interest

The authors declare that they have no conflicts of interest with the contents of this article.

Please see the following file for the referencesReferences for top paper

From a 2015 Clinical Cancer Research paper:

Phase 1 clinical pharmacology study of F14512, a new polyamine-vectorized anti-cancer drug, in naturally occurring canine lymphoma

Dominique Tierny 1, Francois Serres 1, Zacharie Segaoula 1, Ingrid Bemelmans 1, Emmanuel Bouchaert 1,

Aurelie Petain 2, Viviane Brel 3, Stephane Couffin 4, Thierry Marchal 5, Laurent Nguyen 6, Xavier Thuru 7,

Pierre Ferre 2, Nicolas Guilbaud 8, and Bruno Gomes 9,*

Abstract

Purpose: F14512 is a new topoisomerase II inhibitor containing a spermine moiety that facilitates selective uptake by tumor cells and increases topoisomerase II poisoning. F14512 is currently in Phase I/II clinical trial in patients with acute myeloid leukemia. The aim of this study was to investigate F14512 potential in a new clinical indication. Because of the many similarities between human and dog lymphomas, we sought to determine the tolerance, efficacy, PK/PD relationship of F14512 in this indication, and potential biomarkers that could be translated into human trials. Experimental design: Twenty-three dogs with stage III-IV naturally occurring lymphomas were enrolled in the Phase 1 dose-escalation trial which consisted of three cycles of F14512 intravenous injections. Endpoints included safety and therapeutic efficacy. Serial blood samples and tumor biopsies were obtained for PK/PD and biomarker studies. Results: Five dose levels were evaluated in order to determine the recommended dose. F14512 was well tolerated, with the expected dose-dependent hematological toxicity. F14512 induced an early decrease of tumoral lymph node cells, and a high response rate of 91% (21/23) with 10 complete responses, 11 partial responses, 1 stable disease and 1 progressive disease. Phosphorylation of histone H2AX was studied as a potential pharmacodynamic biomarker of F14512. Conclusions: This trial demonstrated that F14512 can be safely administered to dogs with lymphoma resulting in strong therapeutic efficacy. Additional evaluation of F14512 is needed to compare its efficacy with standards of care in dogs, and to translate biomarker and efficacy findings into clinical trials in humans.

AND From ASCO 2015 Annual Meeting

Survival impact of switching to different topoisomerase I or II inhibitors-based regimens (topo-I or topo-II) in extensive-disease small cell lung cancer (ED-SCLC): supplemental analysis from JCOG0509.

Abstract:

Background: The J0509 (phase III study for chemotherapy-naive ED-SCLC) demonstrated amrubicin plus cisplatin (AP) was inferior to irinotecan plus cisplatin (IP). However, median overall survival (OS) of both AP and IP (15 and 17 mo) was more favorable than those of previous trials (9-12 mo), probably because switching to different topo-I or topo-II in the second-line therapy, especially the use of topo-II in IP arm, was frequent. This analysis aimed to investigate whether observed survival benefit of IP arm can be explained by the treatment switching, and how post-protocol chemotherapy affected the result of J0509. Methods: Two analysis sets from J0509 were used: all randomized 283 pts and 250 pts who received post-protocol chemotherapy. One pt without initiation date of second-line therapy was excluded. A rank-preserving structural failure time (RPSFT) model was used to estimate “causal survival benefit” that would have been observed if all pts had been followed with the same type of regimen as randomized throughout the follow-up period. Additionally, to assess the survival impact of second-line use of topo-II, OS after initiating second-line therapy (OS2) was analyzed by multivariate Cox models. Results: %treatment switching in IP arm and AP arm was 65.2% (92/141) and 43.7% (62/142). By RPSFT model, estimated OS excluding the effect of the treatment switching was 2.7-fold longer in IP (topo-I) arm than AP (topo-II) arm. This causal survival benefit was stronger than the original report of J0509 (nearly 1.4-fold extension by Cox model), indicating that re-challenging topo-I in IP arm appeared beneficial. The multivariate Cox analysis for OS2 (n = 250) revealed second-line use of topo-II was detrimental (hazard ratio, 1.5; 95%CI, 1.1-2.1). Among sensitive relapsed pts in IP arm, OS2 was favorable in the following order: irinotecan-based regimen > the other topo-I > topo-II. Conclusions: IP remains the standard therapy. Re-challenging topo-I, especially irinotecan-based topo-I, seemed beneficial for IP-sensitive pts. This result should be confirmed in further investigations with large sample size. Clinical trial information: 000000720.

Below is actively recruiting clinical trials evaluating topoisomerase inhibitors. Shown are only a few trials for a complete list from CancerTrials.gov please see this link:

https://clinicaltrials.gov/ct2/results?term=topoisomerase+inhibitor&recr=Open#wrapper

A service of the U.S. National Institutes of Health

897 studies found for: topoisomerase inhibitor | Open Studies

Include only open studies Exclude studies with Unknown status

Status

Study

Recruiting

A Study of Standard Treatment +/- Enoxaparin in Small Cell Lung Cancer

Condition:	Small Cell Lung Cancer
Interventions:	Drug: cisplatinum or carboplatin and e.g.etoposide.; Drug: cisplatinum or carboplatin and e.g.etoposide+enoxaparin

Recruiting

A Phase I Study of Indenoisoquinolines LMP400 and LMP776 in Adults With Relapsed Solid Tumors and Lymphomas

Conditions:	Neoplasms; Lymphoma
Interventions:	Drug: LMP 400; Drug: LMP 776

Recruiting

A Dose-Ranging Study Evaluating the Efficacy, Safety, and Tolerability of GSK2140944 in the Treatment of Uncomplicated Urogenital Gonorrhea Caused by Neisseria Gonorrhoeae

Condition:	Gonorrhea
Intervention:	Drug: GSK2140944

Recruiting

Selinexor in Combination With Irinotecan in Adenocarcinoma of Stomach and Distal Esophagus

Conditions:	Esophageal Cancer; Gastric Cancer
Interventions:	Drug: Selinexor; Drug: Irinotecan

Recruiting

Multimodal Molecular Targeted Therapy to Treat Relapsed or Refractory High-risk Neuroblastoma

Condition:	Neuroblastoma Recurrent
Interventions:	Drug: Dasatinib; Drug: Rapamycin; Drug: Irinotecan; Drug: Temozolomide

Unknown ^†

Study of the Farnesyl Transferase Inhibitor, R115777, in Combination With Topotecan (NYU 99-32)

Condition:	Cancer
Interventions:	Drug: R115777 (farnesyl transferase inhibitor); Drug: Topotecan

Recruiting

Pegylated Irinotecan NKTR 102 in Treating Patients With Relapsed Small Cell Lung Cancer

Condition:	Recurrent Small Cell Lung Carcinoma
Interventions:	Other: Laboratory Biomarker Analysis; Drug: Pegylated Irinotecan; Other: Pharmacological Study

Recruiting

Selinexor and Chemotherapy in Treating Patients With Relapsed or Refractory Acute Myeloid Leukemia

Conditions:	Adult Acute Myeloid Leukemia With 11q23 (MLL) Abnormalities; Adult Acute Myeloid Leukemia With Del(5q); Adult Acute Myeloid Leukemia With Inv(16)(p13;q22); Adult Acute Myeloid Leukemia With t(15;17)(q22;q12); Adult Acute Myeloid Leukemia With t(16;16)(p13;q22); Adult Acute Myeloid Leukemia With t(8;21)(q22;q22); Recurrent Adult Acute Myeloid Leukemia; Secondary Acute Myeloid Leukemia
Interventions:	Drug: mitoxantrone hydrochloride; Drug: etoposide; Drug: cytarabine; Drug: selinexor; Other: laboratory biomarker analysis; Other: pharmacological study

Recruiting

WEE1 Inhibitor MK-1775 and Irinotecan Hydrochloride in Treating Younger Patients With Relapsed or Refractory Solid Tumors

Conditions:	Childhood Solid Neoplasm; Recurrent Childhood Medulloblastoma; Recurrent Childhood Supratentorial Primitive Neuroectodermal Tumor; Recurrent Neuroblastoma
Interventions:	Drug: Irinotecan Hydrochloride; Other: Laboratory Biomarker Analysis; Other: Pharmacological Study; Drug: WEE1 Inhibitor AZD1775

Recruiting

PARP Inhibitor BMN-673 and Temozolomide or Irinotecan Hydrochloride in Treating Patients With Locally Advanced or Metastatic Solid Tumors

Conditions:	Metastatic Cancer; Unspecified Adult Solid Tumor
Interventions:	Drug: PARP inhibitor BMN-673; Drug: temozolomide; Drug: irinotecan hydrochloride; Other: pharmacological study; Other: laboratory biomarker analysis

Recruiting

A Phase II Multicenter, Randomized, Placebo Controlled, Double Blinded Clinical Study of KD018 as a Modulator of Irinotecan Chemotherapy in Patients With Metastatic Colorectal Cancer

Condition:	Colorectal Neoplasms
Interventions:	Drug: KD018; Drug: Irinotecan; Drug: Placebo

Recruiting

The Efficacy of the 7 Days Tailored Therapy as 2nd Rescue Therapy for Eradication of H. Pylori Infection

Condition:	Helicobacter Infection
Interventions:	Procedure: H. pylori culture and antimicrobial susceptibility testing; Drug: 14 days empirical bismuth quadruple therapy (Proton pump inhibitor); Drug: Metronidazole; Drug: Tetracycline; Drug: tripotassium dicitrate bismuthate; Drug: 7 days tailored therapy Proton Pump Inhibitor; Drug: Moxifloxacin; Drug: Amoxicillin

Recruiting

G1T28 (CDK 4/6 Inhibitor) in Combination With Etoposide and Carboplatin in Extensive Stage Small Cell Lung Cancer (SCLC)

Condition:	Small Cell Lung Cancer
Interventions:	Drug: G1T28 + carboplatin/ etoposide; Drug: Placebo + carboplatin/ etoposide

Recruiting

Trial of Topotecan With VX-970, an ATR Kinase Inhibitor, in Small Cell Lung Cancer

Conditions:	Carcinoma, Non-Small -Cell Lung; Ovarian Neoplasms; Small Cell Lung Carcinoma; Uterine Cervical Neoplasms; Carcinoma, Neuroendocrine
Interventions:	Drug: Topotecan; Drug: VX-970

Recruiting

Prospective Analysis of UGT1A1 Promoter Polymorphism for Irinotecan Dose Escalation in Metastatic Colorectal Cancer Patients Treated With Bevacizumab Combined With FOLFIRI as the First-line Setting

Condition:	Metastatic Colorectal Cancer
Interventions:	Genetic: UGT1A1 genotyping (6,6); Genetic: UGTIA1 genotyping (6,7); Genetic: UGTIA1 genotyping (7,7); Genetic: UGT1A1 non-genotyping; Drug: bevacizumab (Avastin); Drug: irinotecan; Drug: Leucovorin; Drug: 5-FU

Recruiting

A Study of the Bruton’s Tyrosine Kinase Inhibitor, PCI-32765 (Ibrutinib), in Combination With Rituximab, Cyclophosphamide, Doxorubicin, Vincristine, and Prednisone in Patients With Newly Diagnosed Non-Germinal Center B-Cell Subtype of Diffuse Large B-Cell Lymphoma

Condition:	Lymphoma
Interventions:	Drug: Ibrutinib; Drug: Placebo; Drug: Rituximab; Drug: Cyclophosphamide; Drug: Doxorubicin; Drug: Vincristine; Drug: Prednisone (or equivalent)

Recruiting

Irinotecan Combination Chemotherapy for Refractory or Relapsed Brain Tumor in Children and Adolescents

Condition:	Brain Tumor
Intervention:	Drug: Irinotecan combination chemotherapy

Recruiting

A Study To Evaluate PF-04449913 With Chemotherapy In Patients With Acute Myeloid Leukemia or Myelodysplastic Syndrome

Condition:	Acute Myeloid Leukemia
Interventions:	Drug: PF-04449913; Drug: Low dose ARA-C (LDAC); Drug: Decitabine; Drug: Daunorubicin; Drug: Cytarabine

Recruiting

Veliparib and Pegylated Liposomal Doxorubicin Hydrochloride in Treating Patients With Recurrent Ovarian Cancer, Fallopian Tube Cancer, or Primary Peritoneal Cancer or Metastatic Breast Cancer

Conditions:	Estrogen Receptor Negative; HER2/Neu Negative; Male Breast Carcinoma; Progesterone Receptor Negative; Recurrent Breast Carcinoma; Recurrent Fallopian Tube Carcinoma; Recurrent Ovarian Carcinoma; Recurrent Primary Peritoneal Carcinoma; Stage IV Breast Cancer; Triple-Negative Breast Carcinoma
Interventions:	Other: Laboratory Biomarker Analysis; Drug: Pegylated Liposomal Doxorubicin Hydrochloride; Other: Pharmacological Study; Drug: Veliparib

Recruiting

A Study To Evaluate Ara-C and Idarubicin in Combination With the Selective Inhibitor Of Nuclear Export (SINE) Selinexor (KPT-330) in Patients With Relapsed Or Refractory AML

Condition:	Acute Myeloid Leukemia (Relapsed/Refractory)
Interventions:	Drug: Selinexor; Drug: Idarubcin; Drug: Cytarabine

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DNA Repair Pioneers Win Nobel

Posted in Genetics & Innovations in Treatment, Genome Biology, tagged DNA repair, genomics, Nobel Prize on October 9, 2015| Leave a Comment »

DNA Repair Pioneers Win Nobel

Larry H. Bernstein, MD, FCAP, Curator

LPBI

Tomas Lindahl, Paul Modrich, and Aziz Sancar have won this year’s Nobel Prize in Chemistry for their work elucidating mechanisms of DNA repair.

By Tracy Vence | October 7, 2015

http://www.the-scientist.com//?articles.view/articleNo/44182/title/DNA-Repair-Pioneers-Win-Nobel/

Tomas Lindahl, Paul Modrich, and Aziz Sancar today (October 7) took the 2015 Nobel Prize in Chemistry for their seminal research on DNA repair. The three scientists share equally in the prize “for having mapped, at a molecular level, how cells repair damaged DNA and safeguard the genetic information,” according to a Nobel Foundation statement.

“All living cells have repair mechanisms . . . to counter DNA damage,” Lindahl said during a Nobel Foundation press conference following the prize announcement. “[DNA damage] can result in a number of diseases, including cancer.” Asked about sharing in a Nobel Prize, he told reporters: “I feel very lucky and proud to be selected.”

Lindahl is a member of the Nobel Prize in Chemistry’s selection committee but did not participate in this year’s prize selection. He is a professor emeritus at the U.K.’s Francis Crick Institute. In the early 1970s, he was among the first to describe base excision repair, a process that works to patch decaying DNA throughout the cell cycle.

“Tomas was a kind of giant in the field and he has made really, really profound contributions to all aspects of DNA repair and DNA decay,” said Lindahl’s colleague Peter Karran of the Francis Crick Institute.

Later, Modrich, a professor of biochemistry and genomics at the Duke University Medical Center in Durham, North Carolina, described mismatch repair, which reduces the frequency of DNA replication-related errors. Sancar, a professor of biochemistry and biophysics at the University of North Carolina School of Medicine in Chapel Hill, described nucleotide excision repair, which cells use to counteract the effects of mutagens.

This year’s prize “is a very timely recognition of the field,” Karran said. “The field has made tremendous contributions to understanding how cancer develops, for example, and these people have made enormous contributions to understanding cancer, as well as to the basic science of DNA.”

Update (7:06 a.m.): Sancar “spent his entire career working in DNA repair,” Christopher Selby, a research assistant professor at the University of North Carolina who has worked in Sancar’s lab since 1987, told The Scientist. “It’s exciting and interesting to see what it takes to get an award like that. . . . I’ve been fairly close with him throughout his career and I [have now] seen firsthand what goes into generating a body of work that goes into that sort of thing.”

Update (7:26 a.m.): “These guys have [made] tremendous, longstanding contributions to DNA repair, which is what keeps us all alive,” David Lilley, a professor of molecular biology at the University of Dundee, U.K., told The Scientist. “DNA is your library in the cell—you’ve gotta repair it, and it’s under massive onslaught. These [DNA repair] mechanisms are tremendously important.”

Update (7:34 a.m.): “I am absolutely thrilled. Paul was really there at the ground level. He really discovered these proteins in the DNA mismatch repair pathway,” said Lorena Beese, a professor of biochemistry at Duke University who has collaborated with Modrich since the mid-1990s. DNA repair “is such an essential area [of research],” Beese told The Scientist. “Mismatch repair, in particular—there are so many questions left on how this essential process works.”

GEN News Highlights

Oct 7, 2015

Nobel Prize in Chemistry Awarded to DNA Repair Researchers

Thomas Lindahl, Ph.D., Paul Modrich, Ph.D., and Aziz Sancar, M.D., Ph.D., have made fundamental contributions to the study of how cells repair DNA and maintain genomic integrity. [N. Elmehed. © Nobel Media 2015]

http://www.genengnews.com/media/images/GENHighlight/Oct7_2015_NElmehedNobelMedia2015_ChemistryNobelPrize3312717921.jpg

Recipients of the Nobel Prize in Chemistry were announced today acknowledging three scientists that made fundamental contributions to the study of how cells repair DNA and maintain genomic integrity.

Each day our DNA is damaged by UV radiation, free radicals, and other carcinogenic substances. However, even without such external attacks, a DNA molecule within the cell is inherently unstable. Thousands of spontaneous changes to a cell’s genome occur on a daily basis and defects can arise when DNA is copied during cell division, a process that occurs several million times every day in the human body.

The reason our genetic material does not disintegrate into complete chemical chaos is that a host of molecular systems continuously monitor and repair DNA.Most cells use three main pathways to repair damage incurred to genetic material.

Thomas Lindahl, Ph.D., emeritus scientist at the Francis Crick Institute in London, was recognized for his discoveries in base excision repair—the pathway that constitutes the bulk of DNA restoration during the cell cycle from alkylation, methylation, and oxidative stress. In the early 1970s, many scientists believed that DNA was an extremely stable molecule, but Dr. Lindahl demonstrated that DNA decays at a rate that ought to have made the development of life on Earth impossible. This insight led him to discover the base excision repair mechanisms.

Paul Modrich, Ph.D., investigator at the Howard Hughes Medical Institute and professor of biochemistry Duke University School of Medicine, was honored for uncovering how cells resolve errors that occur during DNA replication. This so called mismatch repair pathway rectifies base-pairing errors within DNA and defects within this molecular machinery has been shown to increase genomic mutations up to 1,000-fold. Moreover, mismatch repair errors are the cause of the most common form of hereditary colon cancer (HNPCC) and are believed to contribute to the development of a subset of sporadic tumors that occur in a variety of tissues.

Aziz Sancar, M.D., Ph.D., professor of biochemistry and biophysics at the University of North Carolina School of Medicine, was acknowledged for his seminal work on the nucleotide excision repair pathway. Cells use this pathway to repair UV damage to DNA. Individuals born with defects in this repair system will develop skin cancer when exposed to sunlight. Additionally, the cell also utilizes nucleotide excision repair to correct defects caused by mutagenic substances and DNA lesions that create aberrant bulky regions within the helical strand.

These scientists have provided the essential insights into how cells function and maintain their genomic stability—knowledge that integral for the development of new cancer treatments.

sjwilliamspa

Dr. Lindahl was one of my first influencers during research into glycosylases and DNA repair mechanisms. I still remember the academic debates occurring in hallways concerning the existence of the FAPY glycosylase. Very good to see Dr. Lindahl, Dr. Sancar (who contributed greatly) and Dr. Modrich being recognized for their lifelong works. I would wonder why Erol Friedberg was not mentioned though for his contributions to complement factors. However nice to see DNA repair recognized as a pivotal research area.

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DNA mutagenesis and DNA repair

Posted in Genome Biology, tagged Cancer - General, DNA repair, Mutagenesis, radiation damage on September 5, 2015| Leave a Comment »

DNA mutagenesis and DNA repair

Larry H. Bernstein, MD, FCAP, Curator

Leaders in Pharmaceutical Intelligence – Series E (2; 2.11)

Evelyn M. Witkin, born Evelyn Maisel is an American geneticist who was awarded the National Medal of Science for her work on DNA mutagenesis and DNA repair.

She earned her Ph.D. in 1947 with Theodosius Dobzhansky at Columbia University for her Drosophila research. Her interests evolved from Drosophila genetics to bacterial genetics, and she spent the summer of 1944 at Cold Spring Harbor, where she isolated a radiation-resistant mutant of E. coli. Witkin remained at the Carnegie Institution Department of Genetics at Cold Spring Harbor until 1955.

In 1971, she was appointed Professor of Biological Sciences at Douglass College, Rutgers University, and was named Barbara McClintock Professor of Genetics in 1979. Witkin moved to the Wakeman Institute at Rutgers University in 1983. Among her many honors are membership in the National Academy of Sciences (1977), Fellow of the American Association for the Advancement of Science (1980), American Women of Science Award for Outstanding Research, and Fellow of the American Academy of Microbiology. She was largely responsible for creating the field of DNA mutagenesis and DNA repair, which has played an important role in the biochemical sciences and in clinical radiation therapy for cancer. She is a member of the National Academy of Sciences, a Fellow of the American Association for the Advancement of Science, and the American Academy of Arts and Sciences. Dr. Witkin has also received the Thomas Hunt Morgan Medal of the Genetics Society of America in 2000 and the the Wiley Prize.

Oral History

The reason that I got into genetics in the first place, this is while I was an undergraduate [was that] a friend of mine, my first boyfriend, was a Harvard student who was quite a radical and he had gotten hold of [Trofim Denisovich] Lysenko’s papers. And we would read them and you know, Lysenko didn’t believe in the gene. He thought Mendel was a bourgeois nothing and didn’t believe in the gene and all you had to do was manipulate the environment and you could produce anything. And he was in power. You know, to Stalin this sounded great. You know the story. But at any rate, I didn’t know any genetics yet. So this sounded very nice. It would be wonderful to show that you could just manipulate the environment and change things. And I got intrigued and I thought this would be something to look into and my idea was in going into genetics was to test this! Actually it took about a month of genetics at Columbia to realize that he [Lysenko] was completely a fraud, but I never told Dobzhansky until his fiftieth [birthday] party. It was why I got into genetics and why I wanted a Russian advisor! I confessed, and that’s why—he thought it was absolutely hilarious.

When the Demerec lab was built we all had the opportunity to design our own laboratories. That was fun! And mine was right next to Hershey’s and that was a pleasure.

Well, he was an interesting man too. He was rather—you’ve probably heard from others—he was rather reserved and very focused on his work and not very sociable, but extremely generous and kind. And obviously very brilliant! He was very helpful to me.

I could tell you one story about the 1946 symposium, which I don’t know whether you’ve heard. It’s a story about [Salvador] Luria. He was one of the organizers of the program. That was the first symposium after the war and it was the first one on microorganisms and he and some others were getting the program together and he had seen a paper by a woman named Mary Bunting which was published in 1938. [She] worked with bacteria. He was very impressed by that paper. He said that was really the only paper he knows of that does real bacterial genetics before his work with Delbrück. And he said, “She has to be on the program. We have to find her and get her to come to the symposium.” Nobody knew where Mary Bunting was and he did some real hunting. He got other people to work on it, and I remember he was saying at one point, “We can’t have the symposium without her. We have to find her!” Well, they did find her. Her husband was on the faculty at Yale Medical School and they located her there. And she had three young children and was expecting a fourth. That was her Ph.D. Thesis—this paper [that Luria spoke about] She hadn’t been doing any scientific work for awhile and when Luria proposed that she come talk about this work at the symposium she was horrified and said she couldn’t possibly, and doesn’t even remember and “Go away!” And he was very insistent and she did turn up at the symposium and gave this wonderful talk. And it really changed her life forever. I don’t know if you [know], [but] she became the Dean of Radcliffe College.

But what happened at the symposium was, since she was bogged down with babies at Yale, some of the people here who were at Yale—[such as] Ed Tatum, I remember—they arranged for her to have some lab space at Yale and invited her to come and do some work whenever she had time. She came to seminars and caught up with things. And then she got a job when her children were a little bigger. I think her husband died around there too. She became the Dean of the Douglas College at Rutgers and she had done some very good work there in microbiology. And then she went on to become the Dean of Radcliffe and started the Mary Bunting Institute there, which is an institute designed to make it possible for women to resume their scientific careers after they’ve had a break for family reasons. She told me—I called her at one point to verify this because I mentioned this at some meeting, and I think I talked about it at the phage meeting in ’95—and she verified the fact and she said she would never have gone back to work if not for Luria’s having dug her out. Yes, it really shows things about Luria that I’m not sure are known. One is that he’s—he takes it for granted that men and women are equal. It didn’t occur to him that there’s a reason why she shouldn’t be there. And he also is very generous scientifically. He wanted her to have the credit for doing the first real genetics in bacteria.

Well, I guess I met Barbara [McClintock] my very first day here. I stayed at the dormitory and she was living there at the time. I guess I met here in the living room of the dormitory the very first day that I came and we started talking. I found her absolutely fascinating; she told me quite a lot about what she was doing. We became really good friends. And I spent a lot of time visiting her lab, and she developed a habit of calling me whenever she had something especially exciting. These were the years when she was beginning to discover transposition. I would just sort of drop everything and run over and she would show me something that was beginning to make sense to her and it was just such a privilege to be in that relation[ship] with her—to watch this story develop. It was unmistakably convincing as you explained it. You know, not having known very much about maize genetics it wasn’t easy for me to follow. But she was very patient about describing the experiments and she really was very confident about what she was doing.

Harvard geneticist wins Lasker Award for DNA work

Stephen J. Elledge Ph.D. is a Professor of Genetics at the Harvard Medical School. He earned his B.Sc. in chemistry from the University of Illinois at Urbana–Champaign and his Ph.D. in biology from MIT.

Education: Massachusetts Institute of Technology

Awards: Gairdner Foundation International Award, NAS Award in Molecular Biology, Lasker Award 2015

Harvard geneticist Stephen Elledge started his scientific career trying to figure out how to tinker with the DNA of human cells. Instead, he ended up eavesdropping on the process cells use to fix genetic mistakes.

This accidental work led to profound insights into DNA repair relevant to human birth defects, cancer, and aging.

Stephen J. Elledge, the Gregor Mendel Professor of Genetics and of Medicine at Harvard Medical School and Brigham and Women’s Hospital, is a co-recipient, with Evelyn Witkin of Rutgers University, of the 2015 Albert Lasker Basic Medical Research Award. The award, widely considered to be among the most respected in biomedicine, will be presented on Sept. 18 in New York City.

Elledge and Witkin are being honored for their seminal discoveries that have illuminated the DNA damage response, a cellular pathway that senses when DNA is altered and sets in a motion a series of responses to protect the cell. This pathway is critical to a better understanding of many diseases and conditions, such as cancer.

As cells divide and reproduce, they have to make precise copies of their DNA. Typos can doom a fetus, lead to birth defects, and cause cancer as well as symptoms of aging.

Elledge, who is also affiliated with Brigham and Women’s Hospital, uncovered a sequence of events, called a pathway, that protect a cell once its DNA has been damaged or incorrectly copied.

Harvard Medical School and Brigham and Women’s Hospital scientist recognized for discovering DNA repair

“Steve is an amazing scientist, mentor, and colleague,” said Jeffrey S. Flier, dean of Harvard Medical School (HMS). “His insights into the basic mechanisms of the DNA damage response have profoundly enriched our understanding not only of the fundamental genetics of all cellular life, but also of how we conceptualize many diseases and conditions, especially cancer. This distinction is richly deserved, and I am delighted that Steve is being honored for this extraordinary body of work.”

Stephen J. Elledge: Driven by Questions

Harvard geneticist Stephen J. Elledge has been recognized with the Lasker Award for a discovery that illuminates the DNA damage response. This pathway is critical to a better understanding of many diseases and conditions, such as cancer. Co-produced by Harvard Medical School and Brigham and Women’s Hospital.

“We are extremely proud of Steve, who is truly deserving of this recognition,” said Elizabeth G. Nabel, president of Brigham and Women’s Health Care. “Courageous and insatiably inquisitive, he represents the best of Brigham and Women’s and our mission of driving innovation in basic science to improve human health. As a devoted mentor, Steve is deeply committed to guiding the careers of young investigators, ensuring that the next generation of scientists is filled with curious, passionate, and talented researchers.”

Elledge often describes the process by which a cell duplicates itself as akin to the duplication of a small city. It is a vastly complex process that requires many levels of intricate coordination. Each cell contains a detailed blueprint for this entire process: DNA.

But not every duplication results in a perfect copy. That is because each time a cell makes a copy of itself, DNA is vulnerable to damage, not only from faulty cellular processes, but also from such entities as environmental chemicals. As DNA damage accumulates, it profoundly complicates a cell’s ability to make a faithful copy of itself. This can lead to serious illnesses, birth defects, cancer, and other health problems.

Witkin discovered how bacteria respond to DNA damage, detailing the response to UV radiation. Elledge uncovered a DNA-damage-response pathway that operates in more complex organisms, including humans.

Over the years, Elledge and his colleagues elucidated a signaling network that informs a cell when DNA sustains an injury. Called the DNA damage response, this network senses the problem and sends a signal to the rest of the cell so it can properly repair itself; otherwise, severe mutations could occur. As a result, this pathway helps keep the genome stable and suppresses adverse events such as tumor development. When individuals are born with mutations in this pathway, they often have severe developmental defects. If the pathway is interfered with later in life, cancer can result.

In addition to the award in basic medical research, the Lasker Foundation is also presenting awards to individuals in clinical research and in public service.

According to Claire Pomeroy, president of the Albert and Mary Lasker Foundation, this year’s recipients “remind us all that investing in biological sciences and medical research is crucial for our future.”

Joseph L. Goldstein of the University of Texas Southwestern Medical Center and chair of the Lasker Medical Research Awards Jury, added, “The 2015 Lasker winners had bold ideas and pursued novel questions that they tested through fearless experimentation.”

Over the past century, researchers have invested substantial efforts toward understanding the cell cycle. However, only recently have these studies gained a molecular foothold. Leading the research in this field is Stephen J. Elledge, professor of genetics at Harvard Medical School and Brigham and Women’s Hospital in Boston. Playing the dual roles of inventor and investigator, Elledge developed original techniques to define what drives the cell cycle and how cells respond to DNA damage. By using these tools, he and his colleagues have identified multiple genes involved in cell-cycle regulation.

Elledge’s work has earned him many awards, including a 2001 Paul Marks Prize for Cancer Research and a 2003 election to the National Academy of Sciences. In his Inaugural Article (1), published in this issue of PNAS, Elledge and his colleagues describe the function of Fbw7, a protein involved in controlling cell proliferation. These findings add to the growing cache of cell-cycle knowledge with implications for cancer research.

During his junior year abroad at the University of Southampton in England, Elledge gave biology a try by taking an introductory course and a semester of genetics. The classes sparked an interest, which he kept alive by taking a biochemistry class on his return to the United States. It was during his biochemistry lectures that Elledge first heard about recombinant DNA. “I just thought it was fabulous,” he said. “Once biology got down to being molecular, then it intersected with my interests.”

After receiving his bachelor’s degree in 1978, Elledge applied to graduate programs in biology and chemistry. Although he had not yet decided on which field to focus, he chose to continue his studies at the Massachusetts Institute of Technology (MIT) Biology Department. “I didn’t know what I wanted to do, but they had a lot of people, so I figured I’d be able to sort it out,” he said. Elledge ended up working with bacterial geneticist Graham Walker. For his thesis, Elledge studied the error-prone DNA repair mechanism in Escherichia coli called SOS mutagenesis. His work identified and described the regulation of a group of enzymes now know as errorprone polymerases, the first members of which were the umuCD genes in E. coli (2–4).

Elledge’s schedule at MIT allowed him time for side projects, and he used the opportunity to develop a new cloning tool. His creation was spurred by the frustration of unsuccessfully trying to use two existing tools, lambda phage and bacterial plasmid libraries, to clone the umuC gene, which produces proteins necessary for UV and chemical mutagenesis in E. coli. By combining the tools, Elledge invented a technique that allowed him to approach future cloning problems of this type with great rapidity (5). With the new technique, “you could make large libraries in lambda that behave like plasmids. We called them `phasmid’ vectors, like plasmid and phage together,” said Elledge. The phasmid cloning method was an early cornerstone for molecular biology research.

In 1984, Elledge began a postdoctoral fellowship at Stanford University (Stanford, CA) with mentor Ronald Davis. “Davis is an inventor,” said Elledge. “We had a lot in common because I’m interested in developing new technologies and so is he.”

Elledge soon began working on homologous recombination, an important niche in the field of eukaryotic genetics. Working with the yeast genome, Elledge searched for rec A, a gene that allows DNA to recombine homologously. Although he never located rec A, his work accidentally led him to a family of genes known as ribonucleotide reductases (RNRs), which are involved in DNA production (6). Rec A and RNRs share the same last 4 amino acids, which caused an antibody crossreaction in one of Elledge’s experiments. Initially disappointed with the false positives in his hunt for rec A, Elledge was later delighted with his luck. He found that RNRs are turned on by DNA damage (6), and that these genes are regulated by the cell cycle (7). “It was just serendipity,” he said.

Elledge’s work in this area led to a job offer from Baylor College of Medicine, Houston, in 1989. Prior to leaving Stanford, Elledge attended a talk at the University of California, San Francisco, by Paul Nurse, a leader in cell-cycle research who would later win the 2001 Nobel Prize in medicine. Nurse described his success in isolating the homolog of a key human cell-cycle kinase gene, Cdc2, by using a mutant strain of yeast (8). Although Nurse’s methods were primitive, Elledge was struck by the message he carried: that cell-cycle regulation was functionally conserved, and that many human genes could be isolated by looking for complimentary genes in yeast. Elledge then took advantage of his past successes in building phasmid vectors to build a versatile human cDNA library that could be expressed in yeast.

In his first experiments after setting up a laboratory at Baylor, he introduced this library into yeast, screening for complimentary cell-cycle genes. He quickly identified the same Cdc2 gene isolated by Nurse. However, Elledge also discovered a related gene known as Cdk2. Elledge subsequently found that Cdk2 controlled the G₁ to S cell-cycle transition, a step that often goes awry in cancer. These results were published in theEMBO Journal in 1991 (9). “It was one of the biggest papers I’ve had,” said Elledge.

Elledge also continued to capitalize on his unexpected discovery of RNRs and used them to perform genetic screens to identify genes involved in sensing and responding to DNA damage. He subsequently worked out the signal transduction pathways in both yeast and humans that recognize damaged DNA and replication problems (10–12). These “checkpoint” pathways are central to the prevention of genomic instability and a key to understanding tumorigenesis.

Elledge’s research caught the attention of Wade Harper, a new member of Baylor’s biochemistry faculty. Combining their efforts, Harper and Elledge studied the regulation of Cdk2. “I was a geneticist and Wade was a biochemist. Together we were able to accomplish much more than either alone,” said Elledge. Elledge revamped a method for detecting protein interactions, known as the “two-hybrid system,” into a cloning method by combining it with his lambda cloning techniques. By using the new method, Harper and Elledge succeeded in isolating a gene known as p21, which they later identified as part of a family of Cdk2inhibitors. The gene also was cloned by Bert Vogelstein’s laboratory at Johns Hopkins University (Baltimore, MD), who discovered p21 was regulated by the cancer gene p53. Elledge and Vogelstein realized the similarity of their findings after chatting on the phone and published articles back-to-back in Cell in 1993 (13,14).

Elledge and his laboratory continued to look for other human genes that complimented yeast cell-cycle regulators. In 1996, his team identified a conserved motif, the F-box, that is present in some proteins. This motif recognizes specific protein sequences and tags them with ubiquitin for destruction. The buildup of certain proteins can sabotage the cell cycle and bring it to a halt; thus, destroying these proteins keeps cells dividing. Further investigation showed that the F-box sequence is ubiquitous throughout evolution. “There were so many F-box proteins that we figured it was going to be very central,” he said. Since Elledge’s laboratory published its first article on the F-box in 1998 (15), almost a thousand articles have reported investigations of F-box proteins and related ubiquitin ligases. The F-box has been implicated in numerous pathways, including gene expression, the immune response, cell morphology, cancer, and circadian rhythms.

Elledge’s focus still centers on the F-box motif and the roles played by its multitude of variations. In his Inaugural Article, found on page 3338, Elledge and his colleagues (1) describe mouse knockouts missing the gene to create an F-box protein known as Fbw7. Previous research suggested that Fbw7 controls the degradation of cyclin E, a protein that drives cell proliferation. By studying the knockouts, Elledge’s team showed that Fbw7 controls not only the abundance of cyclin E but also Notch protein. Both of these proteins play key roles in regulating mammalian development.

Elledge’s findings add to the growing body of knowledge on how F-box proteins operate in cells. However, with the function of hundreds of different F-box proteins currently unknown, Elledge and his collaborators, including Wade Harper, will have their work cut out for decades more. He and his laboratory plan to continue studying the genetics and genomics of different F-box proteins, elucidating their roles in cell proliferation. Elledge expects that this vast mystery, combined with his regular discoveries, will keep his passion alive. “I’m a scientist. I want to discover new things, and I want to develop new ways of looking at things. That’s what makes me excited, and that’s what I’m interested in,” he said.

This is a Biography of a recently elected member of the National Academy of Sciences to accompany the member’s Inaugural Article on page 3338.

References

Tetzlaff, M. T., Yu, W., Li, M., Zhang, P., Finegold, M., Mahon, K., Harper, J. W., Schwartz, R. J. & Elledge, S. J. (2004) Proc. Natl. Acad. Sci. USA 100 , 3338-3345.

Elledge, S. J. & Walker, G. C. (1983) J. Mol. Biol. 164 , 175-192.

CrossRefMedlineWeb of Science

Elledge, S. J. & Walker, G. C. (1983) J. Bacteriol. 155 , 1306-1315.

Abstract/FREE Full Text

Perry, K., Elledge, S. J., Mitchell, B. B., Marsh, L. & Walker, G. C. (1985) Proc. Natl. Acad. Sci. USA 82 , 4331-4335.

Abstract/FREE Full Text

Elledge, S. J. & Walker, G. C. (1985) J. Bacteriol. 162 , 777-783.

Abstract/FREE Full Text

Elledge, S. J. & Davis, R. W. (1987) Mol. Cell. Biol. 7 , 2783-2793.

Abstract/FREE Full Text

Elledge, S. J. & Davis, R.W. (1990) Genes Dev. 4, 740-751.

Abstract/FREE Full Text

Lee, M. G. & Nurse, P. (1987) Nature 32 , 31-35.

Elledge, S. & Spottswood, M. (1991) EMBO J. 10 , 2653-2659.

MedlineWeb of Science

Zhou, Z. & Elledge, S. J. (1993) Cell 75, 1119-1127.

CrossRefMedlineWeb of Science

Allen, J. B., Zhou, Z., Siede, W., Friedberg, E. C. & Elledge, S. J. (1994) Genes Dev. 8, 2401-2415.

Abstract/FREE Full Text

Zou, L. & Elledge, S. J. (2003) Science 300, 1542-1548.

Abstract/FREE Full Text

Harper, J. W., Adami, G., Wei, N., Keyomarsi, K. & Elledge, S. J. (1993) Cell 75 , 805-816.

CrossRefMedlineWeb of Science

El-Deiry, W. S., Tokino, T., Velculescu, V. E., Levy, D. B., Parsons, R., Trent, J. M., Lin, D., Mercer, W. E., Kinzler, K. W. & Vogelstein, B. (1993) Cell 75, 817-825.

CrossRefMedlineWeb of Science

Bai, C., Sen, P., Hofmann, K., Ma, L., Goebl, M., Harper, J.W. & Elledge, S. J. (1996) Cell 86, 263-274.

CrossRefMedlineWeb of Science

http://news.harvard.edu/gazette/story/2015/09/geneticist-stephen-j-elledge-receives-lasker-award/

https://www.bostonglobe.com/metro/2015/09/08/harvard-geneticist-stephen-elledge-wins-lasker-award-highest-american-honor-for-scientist/P1ul4SUip2zXQh33CrshAM/story.html

http://www.nytimes.com/2015/09/09/health/lasker-awards-go-to-3-scientists-and-doctors-without-borders.html?ref=todayspaper&_r=0

The DNA Damage Response—Self-awareness for DNAThe 2015 Albert Lasker Basic Medical Research Award

Stephen J. Elledge, PhD¹

JAMA Sept 15, 2015; Vol 314, No. 11 http://jama.jamanetwork.com/article.aspx?articleID=2436308&utm_source=Silverchair%20Information%20Systems&utm_medium=email&utm_campaign=MASTER%3AJAMALatestIssueTOCNotification09%2F15%2F2015

The 2015 Albert Lasker Basic Medical Research Award has been presented to Stephen J. Elledge, PhD, for discoveries concerning the DNA-damage response—a fundamental mechanism that protects the genomes of all living organisms. This Viewpoint provides a summary of the role of the DNA damage response in physiologic responses and the importance in human health.

One of the remarkable properties of nature’s most remarkable molecule, DNA, is self-awareness: it can detect information about its own integrity and transmit that information back to itself. The pathway responsible for this impressive ability is known as the DNA damage response (DDR). The first thoughts many scientists have about DNA damage involve the stereotypical DNA repair pathways such as nucleotide excision repair or base excision repair, which identify damaged bases, excise them, and perfectly patch the DNA. However, there is a much higher-level orchestrator of the cellular response to damaged DNA that deals with nonstereotypical and supremely deleterious alterations of DNA structure and distribution of information about their existence.

Particularly deleterious are the events that break both strands of the DNA or disrupt the most vulnerable aspect of the DNA molecule, its replication. These events require the cell to possess the ability to distinguish the myriad possible structures resulting from these events. Furthermore, cells require this knowledge to properly resolve these problems. If this fails, the integrity of the genome is lost and significantly deleterious events can ensue. Much like the brain, which takes sensory input and transduces that information through neural circuitry to effect the proper response, the DDR acts as a sensor that transduces information on the status of the integrity of the genome to elicit the proper response.

The DDR is a form of chemical intelligence. It ensures that the enzymes that have the ability to remodel the structure of DNA—enzymes that are actually dangerous to DNA if used inappropriately—are activated and deployed at the right time and right place to resolve a particular altered DNA structure to maintain genomic integrity.¹ Morever, it is not only the repair enzymes that are the recipients of this information but also many aspects of cellular and organismal physiology.

RESEARCH IN MODEL ORGANISMS UNCOVERS THE DDR

The notion that cells respond to DNA damage has it roots in basic genetic research dating back to the 1940s, in work by Jean Weigle and Evelyn Witkin that contributed to knowledge of the SOS response in bacteria.²Years later my laboratory and others, through genetic research using the yeasts Saccharomyces cerevisiaeand Schizosaccharomyces pombe,discovered the major components of a very complex eukaryotic DDR.³Genetic analysis of the DNA damage–induced transcriptional induction of genes and radiation-sensitive mutants that control cell cycle transitions uncovered the core DDR genes. This provided a foothold for the transition to human cells, in which the significance of this pathway to human health emerged.

TRANSDUCING THE DNA DAMAGE SIGNAL

The core of the DDR is a pair of parallel protein kinase cascades that sense and distribute information about different classes of DNA structures. The ATM branch senses double-strand breaks and the ATR branch senses stalled replication structures and certain double-strand breaks that occur during S phase. ATM and ATR are both protein kinases of the PIKK family and when activated in response to damage, they phosphorylate downstream checkpoint kinases, Chk2 and Chk1, respectively, to transduce the damage signal.

The effect of activation of these pathways is substantial. More than 1000 proteins are altered by the DDR in response to structural alterations in DNA, profoundly altering cellular physiology.⁴ Beyond repair, communicating the information of DNA damage is critical for multicellular organisms in many other ways. The relevance of the DDR to human health is demonstrated by the more than 30 human disease syndromes that result from mutations in DDR genes spanning developmental disorders, neural degeneration, immune dysregulation, progeria, cancer, and other critical diseases.¹ Below are several examples of some of these connections.

ROLES OF THE DDR IN ORGANISMAL PHYSIOLOGY

Immune Cell Function

Cells undergoing immunoglobulin and T-cell receptor rearrangement experience programmed double-strand breaks and require the DDR to properly execute these recombination events. ATM activation after initial cleavage of one allele results in the repositioning of the other allele to the nuclear periphery to ensure monoallelic recombination.¹ ATM also arrests the cell cycle in response to programmed breaks to ensure recombination prior to S-phase entry. If S-phase entry occurs before the breaks are repaired, it can promote translocations. Immune deficiency also arises from mutations in several DDR genes including the RNF168gene responsible for RIDDLE syndrome, characterized by radiosensitivity, immunodeficiency, dysmorphic features, and learning difficulties.

Brain Development and Neural Degeneration

Mutations in multiple DDR components lead to developmental defects. Brain development in particular appears to be especially sensitive to defects in DNA repair and DDR function. Hypomorphic alleles of ATRcause Seckel syndrome, which is characterized by dwarfism, severe microcephaly, and facial malformation and mental retardation. Microcephaly is also associated with mutations in NBN and MRE11, both regulators of the ATM branch of the DDR, and mutations in MCPH1/BRIT1.¹

Mutations in the ATM gene result in ataxia telangiectasia, a debilitating disease in which progressive loss of purkinjee cells in the cerebellum leads to ataxia. Patients with ataxia telangiectasia also develop weakened immune systems and high rates of infection and premature mortality.

Hematopoetic Disorders

Mutations in the Fanconi anemia pathway, which is controlled by ATR phosphorylation, results in numerous developmental defects including hematologic abnormalities and bone marrow failure. Patients with Fanconi anemia experience increased frequencies of myelodysplastic syndrome, and many develop acute myelogenous leukemia.

Responding to Viral Infections

A complex relationship exists between viral infection and the DDR. Many DNA viruses, including adenovirus, Kaposi sarcoma–associated herpesvirus, hepatitis B virus, and Epstein-Barr virus, activate the DDR because viral replication intermediates resemble DNA damage. Viruses may also indirectly activate the DDR by expressing oncoproteins that force cells into S phase and generate replicative stress. The DDR can signal directly to the immune system by inducing ligands for the NKG2D and DNAMA-1 receptors⁵expressed on natural killer cells and CD8⁺ T cells, both of which are capable of killing cells and contributing to antiviral immunity. In some cases, viruses such as SV40 have grown to depend on the DDR, and other viruses such as adenoviruses go to great lengths to inactivate the DDR, underscoring its role in controlling viral function.

The DDR and Cancer

The DDR is highly relevant to all aspects of cancer.⁶ Most critically, DDR function promotes genomic stability. Loss of a large number of DDR genes result in increased frequencies of cancer; these include ATM,NBS1, p53, BRCA1, BRCA2, PALB2, BRIP, BLM, WRN, MCPH1, 53BP1, ATR, CHK1, CHK2, and numerous Fanconi anemia genes whose loss enhance the frequencies of alterations in classical tumor suppressors and oncogenes. Second, the DDR is also relevant to the effectiveness of classic therapeutic treatments, such as radiotherapy and chemotherapy, because these therapies are based on induction of DNA damage, which triggers DDR-dependent cell death, particularly in proliferating cells. Because many tumors become defective in some aspect of the DDR, they become more dependent on other DDR or DNA repair components, and cancer therapies directed at inhibiting key components like CHK1, ATR, or PARP are being evaluated in clinical trials.⁶

Aging and Telomeres

Another critical sensory event occurs when somatic cells exceed their intended proliferative lifetimes, such as in the early stages of cancer. In these cells telomeric ends of chromosomes shorten and are sensed as DNA damage, activating the DDR. Telomere shortening also occurs in a normal physiological setting with aging. Under these conditions, DDR activation informs the cell such that it may choose to undergo apoptosis or a differentiation pathway called senescence, both potent tumor suppressive mechanisms. Senescence relies on 2 of the most potent tumor suppressors, p53 and p16.⁷ Importantly, the accumulation of senescent cells has been implicated in acceleration of aging and age-related diseases. Senescent cells secrete cytokines and chemokines and contribute to progressive chronic inflammation, which may contribute to aging and age-related diseases. Removing senescent cells reduces aging in mice.⁷ Thus, the DDR is a 2-edged sword. On the one hand it acts as a barrier to tumorigenesis and on the other hand it acts to promote aging and aging-related diseases.

CONCLUSIONS

The significance of the DDR to human health is clear. Further highlighting its importance is that the loss of the most central components make it impossible to make, not only an organism, but even a cell. Thus, the self-awareness afforded to the DNA molecule by the sensory and information distribution system known as the DDR is critical for the health and survival of the human species. This once again underscores the importance to human health of basic research in model organisms.

ARTICLE INFORMATION

Corresponding Author: Stephen J. Elledge, PhD, Department of Genetics, Harvard Medical School, 77 Ave Louis Pasteur, Room 158D, NRB, Boston, MA 02115 (selledge@genetics.med.harvard.edu).

Published Online: September 8, 2015. doi:10.1001/jama.2015.10387.

Conflict of Interest Disclosures: The author has completed and submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest and none were reported.

REFERENCES

1 Ciccia A, Elledge SJ. The DNA damage response: making it safe to play with knives. Mol Cell. 2010;40(2):179-204.
PubMed | Link to Article

2 Janion C. Inducible SOS response system of DNA repair and mutagenesis in Escherichia coli. Int J Biol Sci. 2008;4(6):338-344.
PubMed | Link to Article

3 Elledge SJ. Cell cycle checkpoints: preventing an identity crisis. Science. 1996;274(5293):1664-1672.
PubMed | Link to Article

4 Matsuoka S, Ballif BA, Smogorzewska A, et al. ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage. Science. 2007;316(5828):1160-1166.
PubMed | Link to Article

5 Cerboni C, Fionda C, Soriani A, et al. The DNA damage response: a common pathway in the regulation of NKG2D and DNAMA-1 ligand expression in normal, infected, and cancer cells. Front Immunol. 2014;4:508.
PubMed | Link to Article

6 Lord CJ, Ashworth A. The DNA damage response and cancer therapy. Nature. 2012;481(7381):287-294.
PubMed | Link to Article

7 van Deursen JM. The role of senescent cells in ageing. Nature. 2014;509(7501):439-446.
PubMed | Link to Article

Novel Protein May Open Door to New Therapies for Infection and Cancer

GEN News Aug 28, 2015 http://www.genengnews.com/gen-news-highlights/novel-protein-may-open-door-to-new-therapies-for-infection-and-cancer/81251675/

Scientists at Florida State University say they have taken a critical step forward in the fight against cancer with a discovery that could open up the door for new research and treatment options.

Fanxiu Zhu, Ph.D., the FSU Margaret and Mary Pfeiffer Endowed Professor for Cancer Research, and his team uncovered a viral protein in the cell that inhibits the major DNA sensor and thus the body’s response to viral infection, suggesting that this cellular pathway could be manipulated to help a person fight infection, cancer, or autoimmune diseases. They named the protein KicGas.

“We can manipulate the protein and/or the sensor to boost or tune down the immune response in order to fight infectious and autoimmune diseases, as well as cancers,” said Dr. Zhu, whose study (“Inhibition of cGAS-cGAMP DNA-Sensing Signaling by a Herpesvirus Virion Protein”) was published in Cell Host and Microbe.

Dr. Zhu leads a research team investigating how DNA viruses can cause cancer. About 15% of human cancer cases are caused by viruses, so scientists have been seeking answers about how the body responds to viral infection and how some viruses maintain life-long infections.

In the past few years, researchers finally identified the major DNA sensor in cells, known as cGas. That spurred researchers to further examine this sensor in the context of human disease because ideally that sensor should have been alerting the body to fight disease brought by a DNA virus.

Although people are equipped with sophisticated immune systems to cope with viral infection, many viruses have co-evolved mechanisms to evade or suppress the body’s immune responses. So the discovery of this protein is critical to further exploration of how these DNA viruses work and how they can be thwarted.

To uncover this protein, Dr. Zhu’s team studies Kaposi’s sarcoma-associated herpesvirus (KSHV), a human herpesvirus that causes some forms of lymphoma and Kaposi’s sarcoma, a cancer commonly occurring in AIDS patients and other immunocompromised individuals.

In this study, researchers screened every protein in a KSHV cell (90 in total) and ultimately found that one of them directly inhibited the DNA sensor called cGAS. They infected human cell lines with the Kaposi’s sarcoma virus to mimic natural infection, and found when they eliminated the inhibitor protein (KicGas) the cells produced a much stronger immune response.

To do this work, Dr. Zhu collaborated with several scientists both in the U.S. and Germany, including Hong Li, Ph.D., FSU professor of chemistry and biochemistry.

Dr. Li, whose focuses are molecular biology and molecular biophysics, specifically examined how the protein inhibited the cGAS activity in test tubes. For the next phase of research, she is building a three-dimensional model of the interactions to help them better understand how the inhibitor functions.

“These are hard problems to solve, and there is still much to learn here,” Dr. Li said. Learning how the inhibitor functions is a big next step, though. “Once we figure that out, we can hopefully design something to fight the disease,” according to Dr. Zhu.

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Good and Bad News Reported for Ovarian Cancer Therapy

Posted in Biological Networks, Gene Regulation and Evolution, CANCER BIOLOGY & Innovations in Cancer Therapy, Cancer Prevention: Research & Programs, Cell Biology, Signaling & Cell Circuits, Computational Biology/Systems and Bioinformatics, Disease Biology, Small Molecules in Development of Therapeutic Drugs, FDA Regulatory Affairs, FDA, CE Mark & Global Regulatory Affairs: process management and strategic planning - GCP, GLP, ISO 14155, Health Economics and Outcomes Research, Personalized and Precision Medicine & Genomic Research, Pharmaceutical Drug Discovery, Pharmaceutical Industry Competitive Intelligence, Pharmaceutical R&D Investment, Population Health Management, Genetics & Pharmaceutical, Translational Science, Uncategorized, tagged AstraZeneca, BRCA mutation, BRCA1, BRCA2, breast cancer, Cancer - General, Chemotherapy, Clinical trial, Conditions and Diseases, DNA repair, National Institutes of Health, olaparib, ovarian cancer, PARP-1 inhibitor, Pfizer, Prostate cancer, research on July 1, 2014| Leave a Comment »

Good and Bad News Reported for Ovarian Cancer Therapy

Reporter, Curator: Stephen J. Williams, Ph.D.

In a recent Fierce Biotech report

“FDA review red-flags AstraZeneca’s case for ovarian cancer drug olaparib”,

John Carroll reports on a disappointing ruling by the FDA on AstraZeneca’s PARP1 inhibitor olaparib for maintenance therapy in women with cisplatin refractory ovarian cancer with BRCA mutation. Early clinical investigations had pointed to efficacy of PARP inhibitors in ovarian tumors carrying the BRCA mutation. The scientific rationale for using PARP1 inhibitors in BRCA1/2 deficiency was quite clear:

DNA damage can result in

1. double strand breaks (DSB)

DSB can be repaired by efficient homologous recombination (HR) or less efficient non-homologous end joining (NHEJ)

b. BRCA1 involved in RAD51 dependent HR at DSB sites

In BRCA1 deficiency DSB repaired by less efficient NHEJ

2. single strand breaks, damage (SSB)

PARP1 is activated by DNA damage and poly-ADP ribosylates histones and other proteins marking DNA for SSB repair
SSB repair usually base excision (BER) or sometimes nucleotide excision repair (NER)

B. if PARP inhibited then SSB gets converted to DSB

C. in BRCA1/2 deficient background repair is forced to less efficient NHEJ thereby perpetuating some DNA damage pon exposure to DNA damaging agent

A good review explaining the pharmacology behind the rationale of PARP inhibitors in BRCA deficient breast and ovarian cancer is given by Drs. Christina Annunziata and Susan E. Bates in PARP inhibitors in BRCA1/BRCA2 germline mutation carriers with ovarian and breast cancer

(http://f1000.com/prime/reports/b/2/10/) and below a nice figure from their paper:

(from Christina M Annunziata and Susan E Bates. PARP inhibitors in BRCA1/BRCA2 germline mutation carriers with ovarian and breast cancer. F1000 Biol Reports, 2010; 2:10.) Creative Commons

Dr. Sudipta Saha’s post BRCA1 a tumour suppressor in breast and ovarian cancer – functions in transcription, ubiquitination and DNA repair discusses how BRCA1 affects the double strand DNA repair process, augments histone modification, as well as affecting expression of DNA repair genes.

Dana Farber’s Dr. Ralph Scully, Ph.D., in Exploiting DNA Repair Targets in Breast Cancer (http://www.dfhcc.harvard.edu/news/news/article/5402/), explains his research investigating why multiple DNA repair pathways may have to be targeted with PARP therapy concurrent with BRCA1 deficiency.

However FDA investigators voiced their skepticism of AstraZeneca’s clinical results, namely

Small number of patients enrolled
BRCA1/2 cohort were identified retrospectively
results skewed by false benefit from “underperforming” control arm
possible inadvertent selection bias
hazard ratio suggesting improvement in progression free survival but higher risk/benefit

The FDA investigators released their report two days before an expert panel would be releasing their own report (reported in the link below from FierceBiotech)

UPDATED: FDA experts spurn AstraZeneca’s pitch for ovarian cancer drug olaparib

in which the expert panel reiterated the findings of the FDA investigators. The expert panel’s job was to find if there was any clinical benefit for continuing consideration of olaparib, basically stating

“This trial has problems,” noted FDA cancer chief Richard Pazdur during the panel discussion. If investigators had “pristine evidence of a 7-month advantage in PFS, we wouldn’t be here.”

The expert panel was concerned for the above reasons as well as the reported handful of lethal cases of myelodysplastic syndrome and acute myeloid leukemia in the study, although the panel noted these patients had advanced disease before entering the trial, raising the possibility that prior drugs may have triggered their deaths.

This was certainly a disappointment as ….

it was at last year’s ASCO (2013) that investigators at Perelman School of Medicine at the University of Pennsylvania and Sheba Medical Center in Tel Hashomer, Israel presented data showing that in 193 cisplatin-refractory ovarian cancer patients carrying a BRCA1/2 mutation, 31% had a partial or complete tumor regression. In addition the study also showed good response in pancreatic and prostate cancer with tolerable side effects.

See here for study details: http://www.uphs.upenn.edu/news/News_Releases/2013/05/domchek/

As John Carrol from FierceBiotech notes, the decision may spark renewed interest by Pfizer of a bid for AstraZeneca as the potential FDA rejection would certainly dampen AstraZeneca’s future growth and profit plans. Last month AstraZeneca’s CEO made the case to shareholders to reject the Pfizer offer by pointing to AstraZeneca’s potential beefed-up pipeline. AstraZeneca had projected olaparib as a potential $2 billion-a-year seller, although some industry analysts see sales at less than half that amount.

A company spokeswoman said the monotherapy use of olaparib for ovarian cancer assessed by the U.S. expert panel this week was only one element of a broad development program.

Please see a table of current oncology clinical trials with PARP1 inhibitors

at end of this post

However, on the same day, FierceBiotechreports some great news (at least in Europe) on the ovarian cancer front:

EU backs Roche’s Avastin for hard-to-treat ovarian cancer

As Arlene Weintraub of FierceBiotech reports:

EU Committee for Medicinal Products for Human Use (CHMP) handed down a positive ruling on Avastin, recommending that the European Commission approve the drug for use in women with ovarian cancer that’s resistant to platinum-based chemotherapy. It’s the first biologic to receive a positive opinion from the CHMP for this hard-to-treat form of the disease.

Please see here for official press release: CHMP recommends EU approval of Roche’s Avastin for platinum-resistant recurrent ovarian cancer

EU had been getting pressure from British doctors to approve Avastin based on clinical trial results although it may be important to note that the EU zone seems to have an ability to recruit more numbers for clinical trials than in US. For instance an EU women’s breast cancer prevention trial had heavy recruitment in what would be considered a short time frame compared to recruitment times for the US.

Below is a table on PARP1 inhibitors in current clinical trials (obtained from NewMedicine’s Oncology KnowledgeBase™). nm|OK is a relational knowledgeBASE covering all major aspects of product development in oncolology. The database comprises 6 modules each dedicated in a specific sector within the oncology field.

PARP1 Inhibitors Currently in Clinical Trials for Ovarian Cancer

Developer and Drug Name	Development Status & Location – Indications
AbbVie Current as of: March 27, 2014 PARP inhibitor: ABT-767	Phase I (begin 5/11, ongoing 2/14) Europe (Netherlands) – solid tumors with BRCA1 or BRCA2 mutations, locally advanced or metastatic • ovarian cancer, advanced or metastatic • fallopian tube cancer, advanced or metastatic • peritoneal cancer, advanced or metastatic
AstraZeneca Affiliate(s): · Myriad GeneticsCurrent as of: June 26, 2014Generic Name: Olaparib Brand Name: Lynparza Other Designation: AZD2281, KU59436, KU-0059436, NSC 747856	Phase I (begin 7/05, closed 9/08) Europe (Netherlands, UK, Poland); phase II (begin 6/07, closed 2/08, completed 5/09) USA, Australia, Europe (Germany, Spain, Sweden, UK), phase II (begin 7/08, closed 2/09) USA, Australia, Europe (Belgium, Germany, Poland, Spain, UK), Israel, phase II (begin 8/08, closed 12/09, completed 3/13) USA, Australia, Canada, Europe (Belgium, France, Germany, Poland, Romania, Spain, Ukraine, UK), Israel, Russia; phase II (begin 2/10, closed 7/10) USA, Australia, Canada, Europe (Belgium, Czech Republic, Germany, Italy, Netherlands, Spain, UK), Japan, Panama, Peru (combination); MAA (accepted 9/13) EU, NDA (filed 2/14) USA – ovarian cancer, advanced or metastatic, BRCA positive • ovarian cancer, recurrent, platinum sensitive • ovarian cancer, advanced, refractory, BRCA1 or BRCA2-associatedPhase I (begin 5/08, ongoing 5/12) USA; phase II (begin 7/08, closed 10/09) Canada – breast cancer, locally advanced, BRCA1/BRCA2-associated or hereditary metastatic or inoperable • ovarian cancer, locally advanced, BRCA1/BRCA2-associated or hereditary metastatic or inoperable • breast cancer, triple-negative, BRCA-positive • ovarian cancer, high-grade serous and/or undifferentiated, BRCA-positive Phase I (begin 10/10, ongoing 1/13) USA (combination) – ovarian cancer, inoperable or metastatic, refractory • breast cancer, inoperable or metastatic, refractory Phase III (begin 8/13) USA, Australia, Brazil, Canada, Europe (France, Italy, Netherlands, Poland, Russia, Spain, UK), Israel, South Korea, phase III (begin 9/13) USA, Australia, Brazil, Canada, Europe (France, Germany, Italy, Netherlands, Poland, Russia, Spain, UK), Israel – ovarian cancer, serous, high grade, BRCA mutated, platinum-sensitive, relapsed, third line, maintenance • ovarian cancer, serous or endometrioid, high grade, BRCA mutated, platinum responsive (PR or CR), maintenance, first line • primary peritoneal cancer, high grade, BRCA mutated, platinum responsive (PR or CR), maintenance • fallopian tube cancer, high grade, BRCA mutated, platinum responsive (PR or
BioMarin Pharmaceutical Current as of: June 14, 2014 PARP inhibitor: BMN-673, BMN673, LT-673	Phase I/II (begin 1/11, ongoing 3/14) USA – solid tumors, advanced, recurrent Phase I (begin 2/13, closed 4/13, completed 5/14) USA – healthy volunteers Phase I/II (begin 11/13) USA – solid tumors, relapsed or refractory, BRCA mutated, second line
BiPar Sciences Current as of: April 16, 2009 Parp inhibitor: BSI-401	Preclin (ongoing 4/09) – solid tumors
Clovis Oncology Affiliate(s): · University of Newcastle Upon Tyne · Cancer Research Campaign Technology · PfizerCurrent as of: June 21, 2014Generic Name: Rucaparib Brand Name: Rucapanc Other Designation: AG140699, AG014699, AG-14,699, AG-14669, AG14699, AG140361, AG-14361, AG-014699, CO-338, PF-01367338	Phase I (begin 03, completed 05) Europe (UK) (combination), phase I (begin 2/10, closed 11/13) Europe (France, UK) (combination) – solid tumors, advanced Phase II (begin 12/07, closed 10/13) Europe (UK) – breast cancer, advanced or metastatic, in patients carrying BRCA1 or BRCA2 mutations • ovarian cancer, advanced or metastatic, in patients carrying BRCA1 or BRCA2 mutations Phase I/II (begin 11/11, ongoing 6/14) USA, Europe (UK) – solid tumors, metastatic, with mutated BRCA • breast cancer, metastatic, HEr2 negative, with mutated BRCA
Sanofi Current as of: June 03, 2013 Generic Name: Iniparib Brand Name: Tivolza Other Designation: BSI-201, NSC 746045, SAR240550	Phase I/Ib (begin 3/06, closed 3/10) USA (combination), phase I (begin 7/10, closed 11/10) USA, phase I (begin 9/10, ongoing 2/11) Japan (combination); phase Ib (begin 1/07, ongoing 1/11) USA (combination) – solid tumors, advanced, refractory Phase II (begin 5/08, closed 1/09) USA – ovarian cancer, advanced, refractory, BRCA-1 or BRCA-2 associated • fallopian tube cancer, advanced, refractory, BRCA-1 or BRCA-2 associated • peritoneal cancer, advanced, refractory, BRCA-1 or BRCA-2 associated
Tesaro Affiliate(s): · MerckCurrent as of: May 18, 2014Generic Name: Niraparib Other Designation: MK-4827, MK4827	Phase I (begin 9/08, closed 2/11) USA, Europe (UK) – solid tumors, locally advanced or metastatic • ovarian cancer, locally advanced or metastatic, BRCA mutant • chronic lymphocytic leukemia (CLL), relapsed or refractory • prolymphocytic leukemia, T cell, relapsed or refractory Phase Ib (begin 11/10, closed 3/11, terminated 10/12) USA (combination) – solid tumors, locally advanced or metastatic • ovarian cancer, serous, high grade, platinum resistant or refractoryPhase III (begin 5/13, ongoing 5/14) USA – ovarian cancer, platinum-sensitive, high grade serous or BRCA mutant, chemotherapy responsive • fallopian tube cancer • primary peritoneal cancer
Teva Pharmaceutical Industries Current as of: May 04, 2013 Designation: CEP-9722	Phase I (begin 5/11, closed 11/12, terminated 10/13) USA, phase I (begin 6/09, closed 7/12, completed 1/12) Europe (France and UK) (combination) – solid tumors, advanced, third line Phase I (begin 5/11, completed 1/13) Europe (France) (combination) – solid tumors, advanced • mantle cell lymphoma (MCL), advanced

Summary of Combination Ovarian Cancer Trials with Avastin (current and closed)

Indication in Development	ovarian cancer, advanced, recurrent, persistent • ovarian cancer, progressive, platinum resistant, second line • fallopian tube cancer, progressive, platinum resistant, second line • primary peritoneal cancer, progressive, platinum resistant, second line
Latest Status	Phase II (begin 4/02, closed 8/04) USA, phase II (begin 11/04, closed 10/05) USA; phase III (begin 10/09) Europe (Belgium, Bosnia and Herzegovina, Denmark, Finland, France, Germany, Greece, Italy, Netherlands, Norway, Portugal, Spain, Sweden), Turkey
Clinical History	Refer to the Combination Trial Module for trials of Avastin in combination with various chemotherapeutic regimens.According to results from the AURELIA clinical trial (protocol ID: MO22224; 2009-011400-33; NCT00976911), the median PFS in women with progressive platinum resistant ovarian, fallopian tube or primary peritoneal cancer treated with Avastin in combination with chemotherapy, was 6.7 months compared to 3.4 months in those treated with chemotherapy alone for an HR of 0.48 (range =0.38–0.60).. In addition, the objective response rate was 30.9% in women treated with Avastin compared to 12.6% in those on chemotherapy (p=0.001). Certain AE (Grade 2 to 5) that occurred more often in the Avastin arm compared to the chemotherapy alone arm were high blood pressure (20% versus 7%) and an excess of protein in the urine (11% versus 1%). Gastrointestinal perforations and fistulas occurred in 2% of women in the Avastin arm compared to no events in the chemotherapy arm (Pujade-Lauraine E, etal, ASCO12, Abs. LBA5002).A multicenter (n=124), randomized, open label, 2-arm, phase III clinical trial (protocol ID: MO22224; 2009-011400-33; NCT00976911; http://clinicaltrials.gov/ct2/results?term=NCT00976911 ), dubbed AURELIA, was initiated in October 2009, in Europe (Belgium, Bosnia and Herzegovina, Denmark, Finland, France, Germany, Greece, Italy, Netherlands, Norway, Portugal, Spain, and Sweden), and Turkey, to evaluate the efficacy and safety of Avastin added to chemotherapy versus chemotherapy alone in patients with epithelial ovarian, fallopian tube or primary peritoneal cancer with disease progression within 6 months of platinum therapy in the first line setting. The trials primary outcome measure is PFS. Secondary outcome measures include objective response rate, biological PFS interval, OS, QoL, and safety and tolerability. According to the protocol, all patients are treated with standard chemotherapy with IV paclitaxel (80 mg/m²) on days 1, 8, 15 and 22 of each 4-week cycle; or IV topotecan at a dose of 4 mg/m² on days 1, 8 and 15 of each 4-week cycle, or 1.25 mg/kg on days 1-5 of each 3-week cycle; or IV liposomal doxorubicin (40 mg/m²) every 4 weeks. Patients (n=179) randomized to arm 2 of the trial are treated with IV Avastin at a dose of 10 mg/kg twice weekly or 15 mg/kg thrice weekly concomitantly with the chemotherapy choice. Treatment continues until disease progression. Subsequently, patients are treated with the standard of care. Patients in arm 1 (n=182), on chemotherapy only may opt to be treated with IV Avastin (15 mg/kg) three times weekly. The trial was set up in cooperation with the Group d’Investigateurs Nationaux pour l’Etude des Cancers Ovariens (GINECO) and was conducted by the international network of the Gynecologic Cancer Intergroup (GCIG) and the pan-European Network of Gynaecological Oncological Trial Groups (ENGOT), under PI Eric Pujade-Lauraine, MD, Hopitaux Universitaires, Paris Centre, Hôpital Hôtel-Dieu (Paris, France). The trial enrolled 361 patients and was closed as of May 2012..Results were presented from a phase II clinical trial (protocol ID: CDR0000068839; GOG-0170D; NCT00022659) of bevacizumab in patients with persistent or recurrent epithelial ovarian cancer or primary peritoneal cancer that was performed by the Gynecologic Oncology Group to determine the ORR, PFS, and toxicity for this treatment. Patients must have been administered 1-2 prior cytotoxic regimens. Treatment consisted of bevacizumab (15 mg/kg) IV every 3 weeks until disease progression or prohibitive toxicity. Between April 2002 and August 2004, 64 patients were enrolled, of which 2 were excluded for wrong primary and borderline histology and 62 were evaluable (1 previous regimen=23, 2 previous regimens=39). The median disease free interval from completion of primary cytotoxic chemotherapy to first recurrence was 6.5 months. Early results demonstrated that some patients had confirmed objective responses and PFS in some was at least 6 months. Observed Grade 3 or 4 toxicities included allergy (Grade 3=1), cardiovascular (Grade 3=4; Grade 4=1), gastrointestinal (Grade 3=3), hepatic (Grade 3=1), pain (Grade 3=2), and pulmonary (Grade 4=1). As of 11/04, 36 patients were removed from the trial, including 29 for disease progression and 1 for toxicity in 33 cases reported. Preliminary evidence exists for objective responses to bevacizumab (Burger R, et al, ASCO05, Abs. 5009).An open label, single arm, 2-stage, phase II clinical trial (protocol ID: AVF2949g, NCT00097019) of bevacizumab in patients with platinum resistant, advanced (Stage III or IV), ovarian cancer or primary peritoneal cancer for whom subsequent doxorubicin or topotecan therapy also has failed was initiated in November 2004 at multiple locations in the USA to determine the safety and efficacy for this treatment.A multicenter phase II clinical trial was initiated in April 2002 to determine the 6-month PFS of patients with persistent or recurrent ovarian epithelial or primary peritoneal cancer treated with bevacizumab (protocol ID: GOG-0170D, CDR0000068839, NCT00022659). IV bevacizumab is administered over 30-90 minutes on day 1. Treatment is repeated every 21 days in the absence of disease progression or unacceptable toxicity. Patients are followed every 3 months for 2 years, every 6 months for 3 years, and then annually thereafter. A total of 22-60 patients will be accrued within 12-30 months. Robert A. Burger, MD, of Chao Family Comprehensive Cancer Center is Trial Chair.This trial was closed in August 2004.

Sources

http://www.fiercebiotech.com/story/fda-review-red-flags-astrazenecas-case-ovarian-cancer-drug-olaparib/2014-06-23

http://www.fiercebiotech.com/story/fda-experts-spurn-astrazenecas-pitch-ovarian-cancer-drug-olaparib/2014-06-25

http://www.fiercepharma.com/story/eu-backs-roches-avastin-hard-treat-ovarian-cancer/2014-06-27

In a followup to this original posting A Report From the Institute of Medicine of the National Academies of Sciences, Engineering, and Medicine entitled

Evolving Approaches in Research and Care for Ovarian Cancers

was generated in a ViewPoint piece in JAMA which discussed their Congressional mandated report on the State of the Science in Ovarian Cancer Research, titled

Ovarian Cancers: Evolving Paradigms in Research and Care

highlights some of the research gaps felt by the committee in the current state of ovarian cancer research including:

consideration in research protocols of the multitude of histologic and morphologic subtypes of ovarian cancer, including the feeling of the committee that high grade serous OVCA originates from the distal end of the fallopian tube (espoused by Dr. Doubeau and Dr. Christopher Crum) versus originating from the ovarian surface epithelium
a call for expanded screening and prevention research with mutimodal screening including CA125 with secondary transvaginal screen
better patient education of the risk/benefit of genetic testing including BRCA1/2 as well as in consideration for PARP inhibitor therapy
treatments should be standardized and disseminated including more research in health outcomes and decision support for personalized therapy

This Perspective article can be found here: jvp160038

Some other posts relating to OVARIAN CANCER on this site include

Efficacy of Ovariectomy in Presence of BRCA1 vs BRCA2 and the Risk for Ovarian Cancer

Testing for Multiple Genetic Mutations via NGS for Patients: Very Strong Family History of Breast & Ovarian Cancer, Diagnosed at Young Ages, & Negative on BRCA Test

Ultrasound-based Screening for Ovarian Cancer

Dasatinib in Combination With Other Drugs for Advanced, Recurrent Ovarian Cancer

BRCA1 a tumour suppressor in breast and ovarian cancer – functions in transcription, ubiquitination and DNA repair

Read Full Post »

Good and Bad News Reported for Ovarian Cancer Therapy

Posted in CANCER BIOLOGY & Innovations in Cancer Therapy, Cancer Prevention: Research & Programs, FDA Regulatory Affairs, Health Economics and Outcomes Research, Medical Devices R&D and Inventions, tagged avastin, BRCA1, breast cancer, Cancer - General, Chemotherapy, DNA repair, European Medicines Agency, FDA approval Denied, Food and Drug Administration, health, ovarian cancer, PARP-1 inhibitor on June 29, 2014| Leave a Comment »

Good and Bad News Reported for Ovarian Cancer Therapy

Reporter, Curator: Stephen J. Williams, Ph.D.

In a recent Fierce Biotech report

“FDA review red-flags AstraZeneca’s case for ovarian cancer drug olaparib”,

John Carroll reports on a disappointing ruling by the FDA on AstraZeneca’s PARP inhibitor olaparib for maintenance therapy in women with cisplatin refractory ovarian cancer with BRCA mutation. Early clinical investigations had pointed to efficacy of PARP inhibitors in ovarian tumors carrying the BRCA mutation. The scientific rationale was quite clear:

A good review explaining the pharmacology behind the rationale of PARP inhibitors in BRCA deficient breast and ovarian cancer is given by Drs. Christina Annunziata and Susan E, Bates in PARP inhibitors in BRCA1/BRCA2 germline mutation carriers with ovarian and breast cancer

(http://f1000.com/prime/reports/b/2/10/)

Dr. Sudipta Saha’s postBRCA1 a tumour suppressor in breast and ovarian cancer – functions in transcription, ubiquitination and DNA repair discusses how BRCA1 affects the double strand DNA repair process, augments histone modification, as well as affecting expression of DNA repair genes.

However FDA investigators voiced their skepticism of AstraZeneca’s clinical results, namely

Small number of patients enrolled
BRCA1/2 cohort were identified retrospectively
results skewed by false benefit from “underperforming” control arm
possible inadvertent selection bias
hazard ratio suggesting improvement in progression free survival but higher risk/benefit

The FDA investigators released their report two days before an expert panel would be releasing their own report (reported in the link below from FierceBiotech)

UPDATED: FDA experts spurn AstraZeneca’s pitch for ovarian cancer drug olaparib

“This trial has problems,” noted FDA cancer chief Richard Pazdur during the panel discussion. If investigators had “pristine evidence of a 7-month advantage in PFS, we wouldn’t be here.”

However, on the same day, FierceBiotechreports some great news (at least in Europe) on the ovarian cancer front:

EU backs Roche’s Avastin for hard-to-treat ovarian cancer

As Arlene Weintraub of FierceBiotechreports:

Please see here for official press release: CHMP recommends EU approval of Roche’s Avastin for platinum-resistant recurrent ovarian cancer

EU had been getting pressure from British doctors to approve Avastin based on clinical trial results although it may be important to note that the EU zone seems to have an ability to recruit more numbers for clinical trials than in US. For instance a wonen’s breast cancer prevention trial had heavy recruitment in what would be considered a short time frame compared to the US.

Sources

http://www.fiercebiotech.com/story/fda-review-red-flags-astrazenecas-case-ovarian-cancer-drug-olaparib/2014-06-23

http://www.fiercebiotech.com/story/fda-experts-spurn-astrazenecas-pitch-ovarian-cancer-drug-olaparib/2014-06-25

http://www.fiercepharma.com/story/eu-backs-roches-avastin-hard-treat-ovarian-cancer/2014-06-27

Some other posts relating to OVARIAN CANCER on this site include

Efficacy of Ovariectomy in Presence of BRCA1 vs BRCA2 and the Risk for Ovarian Cancer

Testing for Multiple Genetic Mutations via NGS for Patients: Very Strong Family History of Breast & Ovarian Cancer, Diagnosed at Young Ages, & Negative on BRCA Test

Ultrasound-based Screening for Ovarian Cancer

Dasatinib in Combination With Other Drugs for Advanced, Recurrent Ovarian Cancer

BRCA1 a tumour suppressor in breast and ovarian cancer – functions in transcription, ubiquitination and DNA repair

Read Full Post »

Cancer Mutations Across the Landscape

Posted in Biological Networks, Gene Regulation and Evolution, CANCER BIOLOGY & Innovations in Cancer Therapy, Cell Biology, Signaling & Cell Circuits, Computational Biology/Systems and Bioinformatics, Disease Biology, Small Molecules in Development of Therapeutic Drugs, Genome Biology, Genomic Testing: Methodology for Diagnosis, Medical and Population Genetics, Molecular Genetics & Pharmaceutical, Personalized and Precision Medicine & Genomic Research, tagged Cancer - General, CANCER BIOLOGY & Innovations in Cancer Therapy, Cancer Genome Atlas, cell signaling, clinical associations, clusters, Cox Proportional Hazards model, DNA, DNA repair, driver mutations, functional associations, gene mutations, mutations across cancer types, prognostic analysis, The Cancer Genome Atlas (TCGA), tumorigenesis, Washington University in St. Louis on November 1, 2013| Leave a Comment »

Cancer Mutations Across the Landscape

Curator: Larry H. Bernstein, MD, FCAP

This is an up-to-date article about the significance of mutations found in 12 major types of cancer.

Word Cloud by Daniel Menzin

UPDATED 4/24/2020 The genomic landscape of pediatric cancers: Curation of WES/WGS studies shows need for more data

Mutational landscape and significance across 12 major cancer types

Cyriac Kandoth¹*, Michael D. McLellan¹*, Fabio Vandin², Kai Ye^1,3, Beifang Niu¹, Charles Lu¹, et al.

¹The Genome Institute, Washington University in St Louis, Missouri 63108, USA. ²Department of Computer Science, Brown University, Providence, Rhode Island 02912, USA. ³Department of Genetics, Washington University in St Louis, Missouri 63108, USA. ⁴Department of Medicine, Washington University in St Louis, Missouri 63108, USA. ⁵Siteman Cancer Center, Washington University in St Louis, Missouri 63108, USA. ⁶Department of Mathematics, Washington University in St Louis, Missouri 63108, USA.

NATURE 17 Oct 2013; 5 0 2 http://dx.doi.org/10.1038/nature12634

The Cancer Genome Atlas (TCGA) has used the latest sequencing and analysis methods to identify somatic variants across thousands of tumours. Here we present data and analytical results for point mutations and small insertions/deletions from 3,281 tumours across 12 tumour types as part of the TCGA Pan-Cancer effort. We illustrate

the distributions of mutation frequencies,
types and contexts across tumour types, and
establish their links to tissues of origin,
environmental/ carcinogen influences, and
DNA repair defects.

Using the integrated data sets, we identified 127 significantly mutated genes from well-knownand emerging cellular processes in cancer.

(for example, mitogen-activated protein kinase, phosphatidylinositol-3-OH kinase,Wnt/b-catenin and receptor tyrosine kinase signalling pathways, and cell cycle control)
(for example, histone, histone modification, splicing, metabolism and proteolysis)

The average number of mutations in these significantly mutated genes varies across tumour types;

most tumours have two to six, indicating that the number of driver mutations required during oncogenesis is relatively small.
Mutations in transcriptional factors/regulators show tissue specificity, whereas
histone modifiers are often mutated across several cancer types.

Clinical association analysis identifies genes having a significant effect on survival, and

investigations of mutations with respect to clonal/subclonal architecture delineate their temporal orders during tumorigenesis.

Taken together, these results lay the groundwork for developing new diagnostics and individualizing cancer treatment

Introduction

The advancement of DNA sequencing technologies now enables the processing of thousands of tumours of many types for systematic mutation discovery. This expansion of scope, coupled with appreciable progress in algorithms^1–5, has led directly to characterization of significant functional mutations, genes and pathways^6–18. Cancer encompasses more than 100 related diseases¹⁹, making it crucial to understand the commonalities and differences among various types and subtypes. TCGA was founded to address these needs, and its large data sets are providing unprecedented opportunities for systematic, integrated analysis.

We performed a systematic analysis of 3,281 tumours from 12 cancer types to investigate underlying mechanisms of cancer initiation and progression. We describe variable mutation frequencies and contexts and their associations with environmental factors and defects in DNA repair. We identify 127 significantlymutated genes (SMGs) from diverse signalling and enzymatic processes. The finding of a TP53-driven breast, head and neck, and ovarian cancer cluster with a dearth of other mutations in SMGs suggests common therapeutic strategies might be applied for these tumours. We determined interactions among mutations and correlated mutations in BAP1, FBXW7 and TP53 with detrimental phenotypes across several cancer types. The subclonal structure and transcription status of underlying somatic mutations reveal the trajectory of tumour progression in patients with cancer.

Standardization of mutation data

Stringent filters (Methods) were applied to ensure high quality mutation calls for 12 cancer types: breast adenocarcinoma (BRCA), lung adenocarcinoma (LUAD), lung squamous cell carcinoma (LUSC), uterine corpus endometrial carcinoma (UCEC), glioblastoma multiforme (GBM), head and neck squamous cell carcinoma (HNSC), colon and rectal carcinoma (COAD, READ),bladder urothelial carcinoma (BLCA), kidney renal clear cell carcinoma (KIRC), ovarian serous carcinoma (OV) and acute myeloid leukaemia (LAML; conventionally called AML) (Supplementary Table 1). A total of 617,354 somatic mutations, consisting of

398,750 missense,
145,488 silent,
36,443 nonsense,
9,778 splice site,
7,693 non-coding RNA,
523 non-stop/readthrough,
15,141 frameshift insertions/deletions (indels) and
3,538 inframe indels,

were included for downstream analyses (Supplementary Table 2).

Distinct mutation frequencies and sequence context

Figure 1a shows that AML has the lowest median mutation frequency and LUSC the highest (0.28 and 8.15 mutations per megabase (Mb), respectively). Besides AML, all types average over 1 mutation per Mb, substantially higher than in pediatric tumours²⁰. Clustering²¹ illustrates that

mutation frequencies for KIRC, BRCA, OV and AML are normally distributed within a single cluster, whereas
other types have several clusters (for example, 5 and 6 clusters in UCEC and COAD/ READ, respectively) (Fig. 1a and Supplementary Table 3a, b).

In UCEC, the largest patient cluster has a frequency of approximately 1.5 mutations per Mb, and

the cluster with the highest frequency is more than 150 times greater.

Multiple clusters suggest that factors other than age contribute to development in these tumours^14,16. Indeed,

there is a significant correlation between high mutation frequency and DNA repair pathway genes (for example, PRKDC, TP53 and MSH6) (Supplementary Table 3c). Notably,
PRKDC mutations are associated with high frequency in BLCA, COAD/READ, LUAD and UCEC, whereas
TP53 mutations are related with higher frequencies in AML, BLCA, BRCA, HNSC, LUAD, LUSC and UCEC (all P < 0.05).

Mutations in POLQ and POLE associate with high frequencies in multiple cancer types; POLE association in UCEC is consistent with previous observations¹⁴.

Comparison of spectra across the 12 types (Fig. 1b and Supplementary Table 3d) reveals that LUSC and LUAD contain increased C>A transversions, a signature of cigarette smoke exposure¹⁰. Sequence context analysis across 12 types revealed

the largest difference being in C>T transitions and C>G transversions (Fig. 1c).

The frequency of thymine 1-bp (base pair) upstream of C>G transversions is markedly higher in BLCA, BRCA and HNSC than in other cancer types (Extended Data Fig. 1). GBM, AML, COAD/READ and UCEC have similar contexts in that

the proportions of guanine 1 base downstream of C>T transitions are between
- 59% and 67%, substantially higher than the approximately 40% in other cancer types.

Higher frequencies of transition mutations at CpG in gastrointestinal tumours, including colorectal, were previously reported²². We found three additional cancer types (GBM, AML and UCEC) clustered in the C>T mutation at CpG, consistent with previous findings of

aberrant DNA methylation in endometrial cancer²³ and glioblastoma²⁴.

BLCA has a unique signature for C>T transitions compared to the other types (enriched for TC) (Extended Data Fig. 1).

Significantly mutated genes

Genes under positive selection, either in individual or multiple tumour types, tend to display higher mutation frequencies above background. Our statistical analysis³, guided by expression data and curation (Methods), identified 127 such genes (SMGs; Supplementary Table 4). These SMGs are involved in a wide range of cellular processes, broadly classified into 20 categories (Fig. 2), including

transcription factors/regulators, histone modifiers, genome integrity, receptor tyrosine kinase signalling, cell cycle, mitogen-activated protein kinases (MAPK) signalling, phosphatidylinositol-3-OH kinase (PI(3)K) signalling, Wnt/ -catenin signalling, histones, ubiquitin-mediatedproteolysis, and splicing (Fig. 2).

The identification of MAPK, PI(3)K and Wnt/ -catenin signaling pathways is consistent with classical cancer studies. Notably, newer categories (for example, splicing, transcription regulators, metabolism, proteolysis and histones) emerge as exciting guides for the development of new therapeutic targets. Genes categorized as histone modifiers (Z = 0.57), PI(3)K signalling (Z = 1.03), and genome integrity (Z = 0.66) all relate to more than one cancer type, whereas

transcription factor/regulator (Z = 0.40), TGF- signalling (Z = 0.66), and Wnt/ -catenin signalling (Z = 0.55) genes tend to associate with single types (Methods).

Notably, 3,053 out of 3,281 total samples (93%) across the Pan-Cancer collection had at least one non-synonymous mutation in at least one SMG. The average number of point mutations and small indels in these genes varies across tumour types, with the highest (^,6 mutations per tumour) in UCEC, LUAD and LUSC, and the lowest (^,2 mutations per tumour) in AML, BRCA, KIRC and OV. This suggests that the numbers of both cancer-related genes (only 127 identified in this study) and cooperating driver mutations required during oncogenesis are small (most cases only had 2–6) (Fig. 3), although large-scale structural rearrangements were not included in this analysis.

Common mutations

The most frequently mutated gene in the Pan-Cancer cohort is TP53 (42% of samples). Its mutations predominate in serous ovarian (95%) and serous endometrial carcinomas (89%) (Fig. 2). TP53 mutations are also associated with basal subtype breast tumours. PIK3CA is the second most commonly mutated gene, occurring frequently (>10%) in most cancer types except OV, KIRC, LUAD and AML. PIK3CA mutations frequented UCEC (52%) and BRCA (33.6%), being specifically enriched in luminal subtype tumours. Tumours lacking PIK3CA mutations often had mutations in PIK3R1, with the highest occurrences in UCEC (31%) and GBM (11%) (Fig. 2).

Many cancer types carried mutations in chromatin re-modelling genes. In particular, histone-lysine N-methyltransferase genes (MLL2 (also known as KMT2D), MLL3 (KMT2C) and MLL4 (KMT2B)) cluster in bladder, lung and endometrial cancers, whereas the lysine (K)-specific demethylase KDM5C is prevalently mutated in KIRC (7%). Mutations in ARID1A are frequent in BLCA, UCEC, LUAD and LUSC, whereas mutations in ARID5B predominate in UCEC (10%) (Fig. 2).

Fig. 1. | Distribution of mutation frequencies across 12 cancer types.

Dashed grey and solid white lines denote average across cancer types and median for each type, respectively. b, Mutation spectrum of six transition (Ti) and transversion (Tv) categories for each cancer type. c, Hierarchically clustered mutation context (defined by the proportion of A, T, C and G nucleotides within ±2bp of variant site) for six mutation categories. Cancer types correspond to colours in a. Colour denotes degree of correlation: yellow (r = 0.75) and red (r = 1).

Fig. 2. The 127 SMGs from 20 cellular processes in cancer identified in and Pan-Cancer are shown, with the highest percentage in each gene among 12 (not shown)

Fig. 3. | Distribution of mutations in 127 SMGs across Pan-Cancer cohort.

Box plot displays median numbers of non-synonymous mutations, with outliers shown as dots. In total, 3,210 tumours were used for this analysis (hypermutators excluded).

Figure 4 | Unsupervised clustering based on mutation status of SMGs. Tumours having no mutation or more than 500 mutations were excluded. A mutation status matrix was constructed for 2,611 tumours. Major clusters of mutations detected in UCEC, COAD, GBM, AML, KIRC, OV and BRCA were highlighted.
Complete gene list shown in Extended Data Fig. 3. (not shown)

Figure 5 | Driver initiation and progression mutations and tumour clonal mutation is in the subclone

Survival Analysis

We examined which genes correlate with survival using the Cox proportional hazards model, first analysing individual cancer types using age and gender as covariates; an average of 2 genes (range: 0–4) with mutation frequency 2% were significant (P<_0.05) in each type (Supplementary Table 10a and Extended Data Fig. 6). KDM6A and ARID1A mutations correlate with better survival in BLCA (P = 0.03, hazard ratio (HR) = 0.36, 95% confidence interval (CI): 0.14–0.92) and UCEC (P = 0.03, HR = 0.11, 95% CI: 0.01–0.84), respectively, but mutations in SETBP1, recently identified with worse prognosis in atypical chronic myeloid leukaemia (aCML)³¹, have a significant detrimental effect in HNSC (P = 0.006, HR = 3.21, 95% CI: 1.39–7.44). BAP1 strongly correlates with poor survival (P = 0.00079, HR = 2.17, 95% CI: 1.38–3.41) in KIRC. Conversely, BRCA2 mutations (P = 0.02, HR = 0.31, 95% CI: 0.12–0.85) associate with better survival in ovarian cancer, consistent with previous reports^32,33; BRCA1 mutations showed positive correlation with better survival, but did not reach significance here.

We extended our survival analysis across cancer types, restricting our attention to the subset of 97 SMGs whose mutations appeared in 2% of patients having survival data in 2 tumour types. Taking type, age and gender as covariates, we found 7 significant genes: BAP1, DNMT3A, HGF, KDM5C, FBXW7, BRCA2 and TP53 (Extended Data Table 1). In particular, BAP1 was highly significant (P = 0.00013, HR = 2.20, 95% CI: 1.47–3.29, more than 53 mutated tumours out of 888 total), with mutations associating with detrimental outcome in four tumour types and notable associations in KIRC (P = 0.00079), consistent with a recent report²⁸, and in UCEC(P = 0.066). Mutations in several other genes are detrimental, including DNMT3A (HR = 1.59), previously identified with poor prognosis in AML³⁴, and KDM5C (HR = 1.63), FBXW7 (HR = 1.57) and TP53 (HR = 1.19). TP53 has significant associations with poor outcome in KIRC (P = 0.012), AML (P = 0.0007) and HNSC (P = 0.00007). Conversely, BRCA2 (P = 0.05, HR = 0.62, 95% CI: 0.38 to 0.99) correlates with survival benefit in six types, including OV and UCEC (Supplementary Table 10a, b). IDH1 mutations are associated with improved prognosis across the Pan-Cancer set (HR = 0.67, P = 0.16) and also in GBM (HR = 0.42, P = 0.09) (Supplementary Table 10a, b), consistent with previous work.³⁵

Driver mutations and tumour clonal architecture

To understand the temporal order of somatic events, we analysed the variant allele fraction (VAF) distribution of mutations in SMGs across AML, BRCA and UCEC (Fig. 5a and Supplementary Table 11a) and other tumour types (Extended Data Fig. 7). To minimize the effect of copy number alterations, we focused on mutations in copy neutral segments. Mutations in TP53 have higher VAFs on average in all three cancer types, suggesting early appearance during tumorigenesis.

It is worth noting that copy neutral loss of heterozygosity is commonly found in classical tumour suppressors such as TP53, BRCA1, BRCA2 and PTEN, leading to increased VAFs in these genes. In AML, DNMT3A (permutation test P = 0), RUNX1 (P = 0.0003) and SMC3 (P = 0.05) have significantly higher VAFs than average among SMGs (Fig. 5a and Supplementary Table 11b). In breast cancer, AKT1, CBFB, MAP2K4, ARID1A, FOXA1 and PIK3CA have relatively high average VAFs. For endometrial cancer, multiple SMGs (for example, PIK3CA, PIK3R1, PTEN, FOXA2 and ARID1A) have similar median VAFs. Conversely, KRAS and/or NRAS mutations tend to have lower VAFs in all three tumour types (Fig. 5a), suggesting NRAS (for example, P = 0 in AML) and KRAS (for example, P = 0.02 in BRCA) have a progression role in a subset of AML, BRCA and UCEC tumours. For all three cancer types, we clearly observed a shift towards higher expression VAFs in SMGs versus non-SMGs, most apparent in BRCA and UCEC (Extended Data Fig. 8a and Methods).

Previous analysis using whole-genome sequencing (WGS) detected subclones in approximately 50% of AML cases^15,36,37; however, analysis is difficult using AML exome owing to its relatively few coding mutations. Using 50 AML WGS cases, sciClone (http://github.com/ genome/sciclone) detected DNMT3A mutations in the founding clone for 100% (8 out of 8) of cases and NRAS mutations in the subclone for 75% (3 out of 4) of cases (Extended Data Fig. 8b). Among 304 and 160 of BRCA and UCEC tumours, respectively, with enough coding mutations for clustering, 35% BRCA and 44% UCEC tumours contained subclones. Our analysis provides the lower bound for tumour heterogeneity, because only coding mutations were used for clustering. In BRCA, 95% (62 out of 65) of cases contained PIK3CA mutations in the founding clone, whereas 33% (3 out of 9) of cases had MLL3 mutations in the subclone. Similar patterns were found in UCEC tumours, with 96% (65 out of 68) and 95% (62 out of 65) of tumours containing PIK3CA and PTEN mutations, respectively, in the founding clone, and 9% (2 out of22) ofKRAS and 14% (1 out of 7) ofNRAS mutations in the subclone (Extended Data Fig. 8b and Supplementary Table 12).

Mutation context (-2 to +2 bp) was calculated for each somatic variant in each mutation category, and hierarchical clustering was then performed using the pairwise mutation context correlation across all cancer types. The mutational significance in cancer (MuSiC)³ package was used to identify significant genes for both individual tumour types and the Pan-Cancer collective. An R function ‘hclust’ was used for complete-linkage hierarchical clustering across mutations and samples, and Dendrix³⁰ was used to identify sets of approximately mutual exclusive mutations. Cross-cancer survival analysis was based on the Cox proportional hazards model, as implemented in the R package ‘survival’ (http://cran.r-project.org/web/ packages/survival/), and the sciClone algorithm (http://github.com/genome/sci-clone) generated mutation clusters using point mutations from copy number neutral segments. A complete description of the materials and methods used to generate this data set and its results is provided in the Methods.

References (20 of 38)

Larson, D. E. et al. SomaticSniper: identification of somatic point mutations in whole genome sequencing data. Bioinformatics 28, 311–317 (2012).
Koboldt, D. C. et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 22, 568–576 (2012).
Dees, N. D. et al. MuSiC: Identifying mutational significance in cancer genomes. Genome Res. 22, 1589–1598 (2012).
Roth, A. et al. JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data. Bioinformatics 28, 907–913 (2012).
Cibulskis, K. et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nature Biotechnol. 31, 213–219 (2013).
Jones, S. et al. Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science 321, 1801–1806 (2008).
Parsons, D. W. et al. An integrated genomic analysis of human glioblastoma multiforme. Science 321, 1807–1812 (2008).
Sjo¨blom, T. etal. The consensuscodingsequences of human breast and colorectal cancers. Science 314, 268–274 (2006).
The Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455, 1061–1068 (2008).
Ding, L. et al. Somatic mutations affect key pathways in lung adenocarcinoma. Nature 455, 1069–1075 (2008).
Wood, L. D. etal. The genomic landscapesof human breast and colorectal cancers. Science 318, 1108–1113 (2007).
The Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature 474, 609–615 (2011).
The Cancer Genome Atlas Network. Comprehensive molecular portraits of human breast tumours. Nature 490, 61–70 (2012).
Cancer Genome Atlas Research Network. Integrated genomic characterization of endometrial carcinoma. Nature 497, 67–73 (2013).
The Cancer Genome Atlas Research Network. Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N. Engl. J. Med. 368, 2059–2074 (2013).
The Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature 487, 330–337 (2012).
Ellis, M. J. et al. Whole-genome analysis informs breast cancer response to aromatase inhibition. Nature 486, 353–360 (2012).
The Cancer Genome Atlas Research Network. Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature 499, 43–49 (2013).
Hanahan, D. & Weinberg, R. A. The hallmarks of cancer. Cell 100, 57–70 (2000).
Downing, J. R. et al. The Pediatric Cancer Genome Project. Nature Genet. 44, 619–622 (2012).

UPDATED 4/24/2020 The genomic landscape of pediatric cancers: Curation of WES/WGS studies shows need for more data

The genomic landscape of pediatric cancers: Implications for diagnosis and treatment

BY E. ALEJANDRO SWEET-CORDERO, JACLYN A. BIEGEL

SCIENCE15 MAR 2019 : 1170-1175

Source: https://science.sciencemag.org/content/363/6432/1170

Abstract

The past decade has witnessed a major increase in our understanding of the genetic underpinnings of childhood cancer. Genomic sequencing studies have highlighted key differences between pediatric and adult cancers. Whereas many adult cancers are characterized by a high number of somatic mutations, pediatric cancers typically have few somatic mutations but a higher prevalence of germline alterations in cancer predisposition genes. Also noteworthy is the remarkable heterogeneity in the types of genetic alterations that likely drive the growth of pediatric cancers, including copy number alterations, gene fusions, enhancer hijacking events, and chromoplexy. Because most studies have genetically profiled pediatric cancers only at diagnosis, the mechanisms underlying tumor progression, therapy resistance, and metastasis remain poorly understood. We discuss evidence that points to a need for more integrative approaches aimed at identifying driver events in pediatric cancers at both diagnosis and relapse. We also provide an overview of key aspects of germline predisposition for cancer in this age group.

Approximately 300,000 children from infancy to age 14 are diagnosed with cancer worldwide every year (1). Some of the cancer types affecting the pediatric population are also seen in adolescents and young adults (AYA), but it has become increasingly clear that cancers in the latter age group have unique biological characteristics that can affect prognosis and therapy (2). Pediatric and AYA cancer patients present with a heterogeneous set of diseases that can be broadly subclassified as leukemias, brain tumors, and non–central nervous system (CNS) solid tumors. These subgroups contain numerous distinct clinical entities, many of which are still poorly characterized from a molecular standpoint.

Recent large-scale genomic analyses have increased our understanding of the genetic drivers of pediatric cancer and have helped to identify new clinically relevant subtypes. These studies have also underscored the distinct nature of the genetic alterations in pediatric and AYA cancers versus adult cancers. Of particular note, the number of somatic mutations in most pediatric cancers is substantially lower than that in adult cancers (3, 4). Exceptions are tumors in children who carry germline mutations that compromise repair of DNA damage (5). For many pediatric cancers, driver events are conditioned on the developmental stage in which the tumor arises. For example, a mutation occurring in one developmental compartment (e.g., a muscle stem cell) may lead to cancer, whereas the same mutation in another compartment does not (6). Pediatric cancer genomes are also characterized by specific patterns of copy number alterations and structural alterations [chromoplexy (7), chromothripsis (8)] that are prognostic indicators in several cancer subtypes. Gene fusion events have long been recognized as oncogenic drivers in many pediatric cancers; however, advanced sequencing technologies have revealed that the number of fusion partners is greater than previously thought, and that previously undetected gene rearrangements may also function as drivers. Finally, germline mutations in a wide spectrum of genes that predispose to cancer appear to play a greater role in pediatric cancer than previously appreciated (9, 10).

Somatic alterations in pediatric cancers

Genome landscape studies

Early large-scale sequencing studies of pediatric cancers identified novel driver genes while also underscoring the overall low mutational burden (11–14). Whole exome sequencing studies of Wilms tumor, T-cell acute lymphoblastic leukemia (TALL), and acute myeloid leukemia (CML) identified some recurring mutations such as

FLT3-IDT
WT1
NUP98-NST1 gene fusion

however many of the driver genes were subtype specific. Other fusion events were seen (by RNASeq) such as

EWS-FL1
Bcr-Abl
MYB-QK1

as well as multiple epigenetic events such as methylations.

REFERENCES

E. Steliarova-Foucher, M. Colombet, L. A. G. Ries, F. Moreno, A. Dolya, F. Bray, P. Hesseling, H. Y. Shin, C. A. Stiller, IICC-3 contributors, International incidence of childhood cancer, 2001-10: A population-based registry study. Lancet Oncol. 18, 719–731 (2017). 10.1016/S1470-2045(17)30186-9pmid:28410997
2. V. Tricoli, D. G. Blair, C. K. Anders, W. A. Bleyer, L. A. Boardman, J. Khan, S. Kummar, B. Hayes-Lattin, S. P. Hunger, M. Merchant, N. L. Seibel, M. Thurin, C. L. Willman, Biologic and clinical characteristics of adolescent and young adult cancers: Acute lymphoblastic leukemia, colorectal cancer, breast cancer, melanoma, and sarcoma. Cancer 122, 1017–1028 (2016). 10.1002/cncr.29871pmid:26849082
3. S. Lawrence, P. Stojanov, P. Polak, G. V. Kryukov, K. Cibulskis, A. Sivachenko, S. L. Carter, C. Stewart, C. H. Mermel, S. A. Roberts, A. Kiezun, P. S. Hammerman, A. McKenna, Y. Drier, L. Zou, A. H. Ramos, T. J. Pugh, N. Stransky, E. Helman, J. Kim, C. Sougnez, L. Ambrogio, E. Nickerson, E. Shefler, M. L. Cortés, D. Auclair, G. Saksena, D. Voet, M. Noble, D. DiCara, P. Lin, L. Lichtenstein, D. I. Heiman, T. Fennell, M. Imielinski, B. Hernandez, E. Hodis, S. Baca, A. M. Dulak, J. Lohr, D.-A. Landau, C. J. Wu, J. Melendez-Zajgla, A. Hidalgo-Miranda, A. Koren, S. A. McCarroll, J. Mora, B. Crompton, R. Onofrio, M. Parkin, W. Winckler, K. Ardlie, S. B. Gabriel, C. W. M. Roberts, J. A. Biegel, K. Stegmaier, A. J. Bass, L. A. Garraway, M. Meyerson, T. R. Golub, D. A. Gordenin, S. Sunyaev, E. S. Lander, G. Getz, G. Getz, Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 499, 214–218 (2013). 10.1038/nature12213pmid:23770567
B. Vogelstein, N. Papadopoulos, V. E. Velculescu, S. Zhou, L. A. Diaz Jr.., K. W. Kinzler, Cancer genome landscapes. Science 339, 1546–1558 (2013). 10.1126/science.1235122pmid:23539594
5. B. Campbell, N. Light, D. Fabrizio, M. Zatzman, F. Fuligni, R. de Borja, S. Davidson, M. Edwards, J. A. Elvin, K. P. Hodel, W. J. Zahurancik, Z. Suo, T. Lipman, K. Wimmer, C. P. Kratz, D. C. Bowers, T. W. Laetsch, G. P. Dunn, T. M. Johanns, M. R. Grimmer, I. V. Smirnov, V. Larouche, D. Samuel, A. Bronsema, M. Osborn, D. Stearns, P. Raman, K. A. Cole, P. B. Storm, M. Yalon, E. Opocher, G. Mason, G. A. Thomas, M. Sabel, B. George, D. S. Ziegler, S. Lindhorst, V. M. Issai, S. Constantini, H. Toledano, R. Elhasid, R. Farah, R. Dvir, P. Dirks, A. Huang, M. A. Galati, J. Chung, V. Ramaswamy, M. S. Irwin, M. Aronson, C. Durno, M. D. Taylor, G. Rechavi, J. M. Maris, E. Bouffet, C. Hawkins, J. F. Costello, M. S. Meyn, Z. F. Pursell, D. Malkin, U. Tabori, A. Shlien, Comprehensive Analysis of Hypermutation in Human Cancer. Cell 171, 1042–1056.e10 (2017). 10.1016/j.cell.2017.09.048pmid:29056344
6. Chen, A. Pappo, M. A. Dyer, Pediatric solid tumor genomics and developmental pliancy. Oncogene 34, 5207–5215 (2015). 10.1038/onc.2014.474pmid:25639868
S. C. Baca, D. Prandi, M. S. Lawrence, J. M. Mosquera, A. Romanel, Y. Drier, K. Park, N. Kitabayashi, T. Y. MacDonald, M. Ghandi, E. Van Allen, G. V. Kryukov, A. Sboner, J.-P. Theurillat, T. D. Soong, E. Nickerson, D. Auclair, A. Tewari, H. Beltran, R. C. Onofrio, G. Boysen, C. Guiducci, C. E. Barbieri, K. Cibulskis, A. Sivachenko, S. L. Carter, G. Saksena, D. Voet, A. H. Ramos, W. Winckler, M. Cipicchio, K. Ardlie, P. W. Kantoff, M. F. Berger, S. B. Gabriel, T. R. Golub, M. Meyerson, E. S. Lander, O. Elemento, G. Getz, F. Demichelis, M. A. Rubin, L. A. Garraway, Punctuated evolution of prostate cancer genomes. Cell 153, 666–677 (2013). 10.1016/j.cell.2013.03.021pmid:23622249
P. J. Stephens, C. D. Greenman, B. Fu, F. Yang, G. R. Bignell, L. J. Mudie, E. D. Pleasance, K. W. Lau, D. Beare, L. A. Stebbings, S. McLaren, M.-L. Lin, D. J. McBride, I. Varela, S. Nik-Zainal, C. Leroy, M. Jia, A. Menzies, A. P. Butler, J. W. Teague, M. A. Quail, J. Burton, H. Swerdlow, N. P. Carter, L. A. Morsberger, C. Iacobuzio-Donahue, G. A. Follows, A. R. Green, A. M. Flanagan, M. R. Stratton, P. A. Futreal, P. J. Campbell, Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell 144, 27–40 (2011). 10.1016/j.cell.2010.11.055pmid:21215367
D. W. Parsons, A. Roy, Y. Yang, T. Wang, S. Scollon, K. Bergstrom, R. A. Kerstein, S. Gutierrez, A. K. Petersen, A. Bavle, F. Y. Lin, D. H. López-Terrada, F. A. Monzon, M. J. Hicks, K. W. Eldin, N. M. Quintanilla, A. M. Adesina, C. A. Mohila, W. Whitehead, A. Jea, S. A. Vasudevan, J. G. Nuchtern, U. Ramamurthy, A. L. McGuire, S. G. Hilsenbeck, J. G. Reid, D. M. Muzny, D. A. Wheeler, S. L. Berg, M. M. Chintagumpala, C. M. Eng, R. A. Gibbs, S. E. Plon, Diagnostic Yield of Clinical Tumor and Germline Whole-Exome Sequencing for Children With Solid Tumors. JAMA Oncol. 2, 616 (2016). 10.1001/jamaoncol.2015.5699pmid:26822237
J. Zhang, M. F. Walsh, G. Wu, M. N. Edmonson, T. A. Gruber, J. Easton, D. Hedges, X. Ma, X. Zhou, D. A. Yergeau, M. R. Wilkinson, B. Vadodaria, X. Chen, R. B. McGee, S. Hines-Dowell, R. Nuccio, E. Quinn, S. A. Shurtleff, M. Rusch, A. Patel, J. B. Becksfort, S. Wang, M. S. Weaver, L. Ding, E. R. Mardis, R. K. Wilson, A. Gajjar, D. W. Ellison, A. S. Pappo, C.-H. Pui, K. E. Nichols, J. R. Downing, Germline Mutations in Predisposition Genes in Pediatric Cancer. N. Engl. J. Med. 373, 2336–2346 (2015). 10.1056/NEJMoa1508054pmid:26580448
T. J. Pugh, O. Morozova, E. F. Attiyeh, S. Asgharzadeh, J. S. Wei, D. Auclair, S. L. Carter, K. Cibulskis, M. Hanna, A. Kiezun, J. Kim, M. S. Lawrence, L. Lichenstein, A. McKenna, C. S. Pedamallu, A. H. Ramos, E. Shefler, A. Sivachenko, C. Sougnez, C. Stewart, A. Ally, I. Birol, R. Chiu, R. D. Corbett, M. Hirst, S. D. Jackman, B. Kamoh, A. H. Khodabakshi, M. Krzywinski, A. Lo, R. A. Moore, K. L. Mungall, J. Qian, A. Tam, N. Thiessen, Y. Zhao, K. A. Cole, M. Diamond, S. J. Diskin, Y. P. Mosse, A. C. Wood, L. Ji, R. Sposto, T. Badgett, W. B. London, Y. Moyer, J. M. Gastier-Foster, M. A. Smith, J. M. Guidry Auvil, D. S. Gerhard, M. D. Hogarty, S. J. M. Jones, E. S. Lander, S. B. Gabriel, G. Getz, R. C. Seeger, J. Khan, M. A. Marra, M. Meyerson, J. M. Maris, The genetic landscape of high-risk neuroblastoma. Nat. Genet. 45, 279–284 (2013). 10.1038/ng.2529pmid:23334666
J. R. Downing, R. K. Wilson, J. Zhang, E. R. Mardis, C.-H. Pui, L. Ding, T. J. Ley, W. E. Evans, The Pediatric Cancer Genome Project. Nat. Genet. 44, 619–622 (2012). 10.1038/ng.2287pmid:22641210
St. Jude Children’s Research Hospital–Washington University Pediatric Cancer Genome Project, Somatic histone H3 alterations in pediatric diffuse intrinsic pontine gliomas and non-brainstem glioblastomas. Nat. Genet. 44, 251–253 (2012). 10.1038/ng.1102pmid:22286216
J. Zhang, L. Ding, L. Holmfeldt, G. Wu, S. L. Heatley, D. Payne-Turner, J. Easton, X. Chen, J. Wang, M. Rusch, C. Lu, S.-C. Chen, L. Wei, J. R. Collins-Underwood, J. Ma, K. G. Roberts, S. B. Pounds, A. Ulyanov, J. Becksfort, P. Gupta, R. Huether, R. W. Kriwacki, M. Parker, D. J. McGoldrick, D. Zhao, D. Alford, S. Espy, K. C. Bobba, G. Song, D. Pei, C. Cheng, S. Roberts, M. I. Barbato, D. Campana, E. Coustan-Smith, S. A. Shurtleff, S. C. Raimondi, M. Kleppe, J. Cools, K. A. Shimano, M. L. Hermiston, S. Doulatov, K. Eppert, E. Laurenti, F. Notta, J. E. Dick, G. Basso, S. P. Hunger, M. L. Loh, M. Devidas, B. Wood, S. Winter, K. P. Dunsmore, R. S. Fulton, L. L. Fulton, X. Hong, C. C. Harris, D. J. Dooling, K. Ochoa, K. J. Johnson, J. C. Obenauer, W. E. Evans, C.-H. Pui, C. W. Naeve, T. J. Ley, E. R. Mardis, R. K. Wilson, J. R. Downing, C. G. Mullighan, The genetic basis of early T-cell precursor acute lymphoblastic leukaemia. Nature 481, 157–163 (2012). 10.1038/nature10725pmid:22237106

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Nrf2 Role in Blocking DNA Damage

Posted in CANCER BIOLOGY & Innovations in Cancer Therapy, tagged Biology, Cancer - General, DNA, DNA repair, Keap1/Nrf2 pathway, NFE2L2, Nrf2, Nrf2 nuclear translocation, oxidative stress, PubMed, Seoul National University on June 21, 2013| Leave a Comment »

Larry H Bernstein, MD, Reporter & Curator
http://pharmaceuticalintelligence.com/2013/06/21/Nrf2 Role in Blocking DNA Damage/lhbern

DNA damage has been a central focus of carcinogenesis. The following is of great interest in this respect.

Nrf2 as a novel molecular target for chemoprevention.

Lee JS, Surh YJ.

Cancer Lett. 2005 Jun 28;224(2):171-84. Epub 2004 Nov 11.

Source

National Research Laboratory of Molecular Carcinogenesis and Chemoprevention, College of Pharmacy, Seoul National University, Shinlim-dong, Kwanak-ku, Seoul 151-742, South Korea.

Abstract

One of the rational and effective strategies for chemoprevention is the blockade of DNA damage caused by carcinogenic insult. This can be achieved either

by reducing the formation of reactive carcinogenic species
or stimulating their detoxification.

A wide spectrum of xenobiotic metabolizing enzymes catalyze both phase I (oxidation and reduction) and phase II biotransformation (conjugation) reactions involved in carcinogen activation and/or deactivation. Several antioxidant-response element (ARE)-regulated gene products such as

glutathione S-transferase,
NAD(P)H:quinone oxidoreductase 1,
UDP-glucuronosyltransferase,
gamma-glutamate cysteine ligase, and
hemeoxygenase-1

are known to mediate detoxification and/or to exert antioxidant functions thereby protecting cells from genotoxic damage.

The transcription of ARE-driven genes is regulated, at least in part,

by nuclear transcription factor erythroid 2p45 (NF-E2)-related factor 2 (Nrf2),
which is sequestered in cytoplasm by Kelch-like ECH-associated protein 1 (Keap1).

Exposure of cells to ARE inducers results in

the dissociation of Nrf2 from Keap1 and
facilitates translocation of Nrf2 to the nucleus,
where it heterodimerizes with small Maf protein, and
binds to ARE,

eventually resulting in the transcriptional regulation of target genes.

The Nrf2-Keap1-ARE signaling pathway can be modulated by several upstream kinases including

phosphatidylinositol 3-kinase,
protein kinase C, and
mitogen-activated protein kinases.

Selected Nrf2-Keap1-ARE activators, such as

oltipraz,
anethole dithiolethione,
sulforaphane,
6-methylsulphinylhexyl isothiocyanate,
curcumin,
caffeic acid phenethyl ester,
4′-bromoflavone, etc.

are potential chemopreventive agents. This mini-review will focus on a chemopreventive strategy directed towards

protection of DNA and other important cellular molecules by
inducing de novo synthesis of phase II detoxifying or antioxidant genes via the Nrf2-ARE core signaling pathway.

PMID: 15914268 [PubMed – indexed for MEDLINE]

Nrf2 Pathway Regulates Multidrug-Resistance-Associated Protein 1 in Small Cell Lung Cancer (plosone.org)
antioxidant advancements (ericalawrencenaturopathy.wordpress.com)
Proteomic Profiling Reveals That Resveratrol Inhibits HSP27 Expression and Sensitizes Breast Cancer Cells to Doxorubicin Therapy (plosone.org)
LKB1 is a master kinase in cancer (pharmastrategyblog.com)
Stopping Tumor Survival In Low-Oxygen Environments (medicalnewstoday.com)

English: Graph of Nrf2 publications (pubmed search) by year (Photo credit: Wikipedia)

Most lifespan influencing genes affect the rate of DNA damage (Photo credit: Wikipedia)

Single-strand and double-strand DNA damage (Photo credit: Wikipedia)

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Reversal of Cardiac Mitochondrial Dysfunction

Posted in Atherogenic Processes & Pathology, Biological Networks, Gene Regulation and Evolution, Cardiovascular Pharmacogenomics, Disease Biology, Small Molecules in Development of Therapeutic Drugs, Frontiers in Cardiology and Cardiovascular Disorders, Genome Biology, HTN, Metabolomics, Molecular Genetics & Pharmaceutical, Nitric Oxide in Health and Disease, Nutrigenomics, Nutrition, Nutritional Supplements: Atherogenesis, lipid metabolism, Origins of Cardiovascular Disease, Personalized and Precision Medicine & Genomic Research, Pharmaceutical Industry Competitive Intelligence, Pharmaceutical R&D Investment, Pharmacogenomics, Pharmacotherapy of Cardiovascular Disease, Population Health Management, Genetics & Pharmaceutical, Population Health Management, Nutrition and Phytochemistry, Proteomics, Stem Cells for Regenerative Medicine, Technology Transfer: Biotech and Pharmaceutical, Uncategorized, tagged ATP, Cardiovascular disease, DNA, DNA repair, Heart Failure, Larry H. Bernstein, Mitochondrial biogenesis, Mitochondrial DNA, Mitochondrion, Muscular dystrophy, oxidative stress, Peroxisome proliferator-activated receptor gamma, Physical exercise, Reactive oxygen species, TFAM, Ventricular remodeling on April 14, 2013| 6 Comments »

Reversal of Cardiac mitochondrial dysfunction

Curator: Larry H Bernstein, MD, FACP

This article is the FOURTH in a four-article Series covering the topic of the Roles of the Mitochondria in Cardiovascular Diseases. They include the following;

Mitochondria and Cardiovascular Disease: A Tribute to Richard Bing, Larry H Bernstein, MD, FACP

http://pharmaceuticalintelligence.com/2013/04/14/chapter-5-mitochondria-and-cardiovascular-disease/

Mitochondrial Metabolism and Cardiac Function, Larry H Bernstein, MD, FACP

http://pharmaceuticalintelligence.com/2013/04/14/mitochondrial-metabolism-and-cardiac-function/

Mitochondrial Dysfunction and Cardiac Disorders, Larry H Bernstein, MD, FACP

http://pharmaceuticalintelligence.com/2013/04/14/mitochondrial-dysfunction-and-cardiac-disorders/

Reversal of Cardiac mitochondrial dysfunction, Larry H Bernstein, MD, FACP

http://pharmaceuticalintelligence.com/2013/04/14/reversal-of-cardiac-mitochondrial-dysfunction/

Mitochondrial metabolism and cardiac function

There is sufficient evidence to suggest that, even with optimal therapy, there is an

attenuation or loss of effectiveness of neurohormonal antagonism as heart failure worsens.

The production of oxygen radicals is increased in the failing heart, whereas

normal antioxidant enzyme activities are preserved.

Mitochondrial electron transport is an enzymatic source of oxygen radical generation and

can be a therapeutic target against oxidant-induced damage in the failing myocardium.

Therefore, future therapeutic targets

must address the cellular and molecular mechanisms that contribute to heart failure.

Furthermore, since fundamental characteristics of the failing heart are

defective mitochondrial energetics and
abnormal substrate metabolism

we might expect that substantial beneﬁt may be derived from the development of therapies aimed at

preserving cardiac mitochondrial function and
optimizing substrate metabolism.

Nutrition and physiological function

Blockade of electron transport in isolated, perfused guinea pig hearts –

before ischaemia with the reversible complex I inhibitor amobarbital

decreased superoxide production and
preserved oxidative phosphorylation in cardiac mitochondria,
decreased myocardial damage.

But when ascorbic acid was administered orally to chronic heart failure patients, there were improvements

in endothelial function but
no improvement in skeletal muscle energy metabolism.

Angiotensin I-converting enzyme (ACE) inhibitors with trandolapril treatment in models of heart failure

appear to preserve mitochondrial function
improving cardiac energy metabolism and
function in rats with chronic heart failure.

Similarly perindopril treatment – in rat skeletal muscle after myocardial infarction -restored :

levels of the mitochondrial biogenesis transcription factors PPARg coactivator-1a and
nuclear respiratory factor-2a, and
prevented mitochondrial dysfunction

Tissue effects of ACE inhibition, such as

decreased oxidative stress and
improved endothelial function,

might activate intracellular signalling cascades that

stimulate mitochondrial biogenesis and
improve energy metabolism.

Clearly, the mechanisms of metabolic regulation by

existing cardioprotective agents require further investigation.

Substrate metabolism in the failing heart

Increased sympathetic drive in heart failure patients causes adipose tissue lipolysis, thus

elevating plasma FFA concentrations.

Myocardial FFA uptake rates are largely determined by circulating FFA concentrations.

In addition to being a major fuel in heart,

fatty acids are ligands for the peroxisome proliferator-activated receptors (PPARs),
- members of the nuclear hormone receptor (NHR) family.

One PPAR subtype, PPARa, is highly expressed in heart and skeletal muscle. PPARs regulate gene expression by

binding to response elements in the promoter region of target genes that control fatty acid metabolism, including

acyl-CoA synthetase,
carnitine palmitoyltransferase (CPT)-1,
long-chain acyl-CoA dehydrogenase, and
uncoupling protein (UCP)3.

It has been known for many years that high plasma FFA concentrations are detrimental to the heart,

increasing oxygen consumption for any given workload.

Decreased myocardial oxygen efﬁciency could result, in part,

from the inherent stoichiometric inefﬁciency of fatty acid oxidation,
which accounts for the consumption of 12% more oxygen per ATP synthesized than glucose oxidation.

High levels of plasma FFAs have been associated with increased cardiac UCP3 levels in patients undergoing CABG(Fig) and

are believed to activate the uncoupling action of UCP3.

http://htmlimg1.scribdassets.com/8o5pfgywg0lyerj/images/4-244729cb6a.jpg

Fig . Metabolic modulation of the failing heart can be achieved by inhibiting mitochondrial beta-oxidation with trimetazidine, or

free fatty acid (FFA) uptake via the carnitine palmitoyltransferase (CPT) system with perhexiline,
- giving rise to more oxygen-efﬁcient glucose oxidation.

Alternatively, CPT is inhibited by malonyl-coenzyme A (CoA),

synthesized from cytosolic acetyl-CoA by acetyl-CoA carboxylase.

Pharmacological inhibition, or mutation, of

malonyl-CoA decarboxylase, which normally converts malonyl-CoA back to acetyl-CoA,
elevates malonyl-CoA levels, inhibiting mitochondrial FFA uptake and thus protects the failing heart.

Nutritional Support for the Mitochondria

Human Studies Animal or In Vitro Studies

Alpha lipoic acid Resveratrol
Co-Enzyme Q10 EgCG
Acetyl-L-Carnitine Curcumin

Lipoic Acid & Acetyl-L-Carnitine

Alpha lipoic acid is known to be a mitochondrial antioxidant that preserves or improves mitochondrial function.

lipoic acid can prevent arterial calcification, and
arterial calcification may be related to mitochondrial dysfunction
methods are under study to increase lipoic acid synthase production, the enzyme responsible for making lipoic acid in the body.

Co-Enzyme Q10

It is well known that statin drugs taken for high cholesterol severely reduce CoQ10 levels, and causes other negative cardiovascular side effects.
A study on CAD patients has shown that over 8 weeks of supplementing with 300mg of CoQ10 reversed

mitochondrial dysfunction (as measured by a reduced lactate:pyruvate ratio) and
improved endothelial function (as measured by increased flow-mediated dilation)

Other Mitochondrial Antioxidants

Other natural compounds that have been shown to have antioxidant effects in the mitochondria include

resveratrol, found in wine and grapes,
curcumin from turmeric and
EGCG, found abundantly in green tea extract.

But no studies have been conducted for these compounds in CVD.

Metabolic syndrome and serum carotenoids: findings of a cross-sectional study
in Queensland, Australia

Metabolic syndrome and serum carotenoids.

T Coyne, TI Ibiebele, PD Baade, CS McClintock and JE Shaw.

Viertel Center for Research in Cancer Control, Cancer Council Queensland, and School of Public Health,

Queensland University of Technology and University of Queensland, Brisbane, Australia

Several components of the metabolic syndrome are known to be oxidative stress-related conditions

diabetes and
cardiovascular disease,

Carotenoids are compounds derived primarily from plants and several have been shown to be potent antioxidant nutrients.

Both diabetes and cardiovascular disease are known to be oxidative stress-related conditions such that

antioxidant nutrients may play a protective role in these conditions.

Several cross–sectional surveys have found lower levels of serum carotenoids among those with impaired glucose metabolism or type 2 diabetes.

Carotenoids are compounds derived primarily from plants, several of which are known to be potent antioxidants.

Epidemiological evidence indicates that some serum carotenoids may play a protective role against the development of chronic diseases such as

atherosclerosis,
stroke,
hypertension,
certain cancers,
inflammatory diseases and
diabetic retinopathy.

The primary carotenoids found in human serum are

α-carotene
β-carotene
β-cryptoxanthin
lutein/zeaxanthin
lycopene.

The aim of this study was to examine the associations between metabolic syndrome status and major serum carotenoids in adult Australians.

Data on the presence of the metabolic syndrome, based on International Diabetes Federation 2005 criteria, were collected from 1523 adults

aged 25 years and over in six randomly selected urban centers in Queensland, Australia, using a cross sectional study design.

The following were determined:

Weight
height
BMI
waist circumference
blood pressure
fasting and 2-34 hour blood glucose
lipids
five serum carotenoids.

Criteria used to assess the number of metabolic syndrome components present in a 171 participant using the

2005 International Diabetes Federation definition are as follows:
Components = 0 -none of the metabolic syndrome components (i.e. abdominal obesity, raised triglyceride,

reduced HDL-cholesterol, raised blood pressure, and impaired fasting plasma glucose) are present;

Components = any 1 one of the five metabolic syndrome components is present ;
Components = 2 – any two of the five components are present;
Components = 3 any three of the components are present;
Components = 4 – any four of the components are present;
Components = 5 = all five metabolic syndrome components are present.

This study investigated the relationships between these five primary serum carotenoids and the metabolic syndrome

in a cross-sectional population-based study in Queensland, Australia. Distributions of serum carotenoids were skewed

and therefore natural logarithmically transformed to better approximate the normal distribution for regression analyses.

Association between log transformed serum carotenoids as dependent variables and metabolic syndrome status were

assessed using multiple linear regression analysis. Results are reported as back transformed geometric means.

Analysis was performed for each serum carotenoid separately, and the sum of the five carotenoids,

adjusting for the following potential confounders:

age
sex
education
BMI
smoking
alcohol intake
physical activity
vitamin use.

Mean serum alpha-carotene, beta-carotene and the sum of the five carotenoid concentrations were significantly lower (p<0.05)

in persons with the metabolic syndrome (after adjusting for age,sex, education, BMI status, alcohol intake, smoking, physical activity

status and vitamin/mineral use) than persons without the syndrome. Alpha, beta and total carotenoids also decreased significantly

(p<0.05) with increased number of components of the metabolic syndrome, after adjusting for these confounders. These differences

were significant among former smokers and non-smokers, but not in current smokers. Low concentrations of serum

alpha-carotene,
beta carotene and
the sum of five carotenoids

appear to be associated with metabolic syndrome status.

The overall prevalence of the syndrome was 24% and was significantly higher among males than females. As would be expected, significant

differences in prevalence of the syndrome were seen with

body mass index
waist circumference
systolic and diastolic blood pressure
blood lipids.

Significant differences were also evident by

age group, smoking status, educational status and income.

Income was marginally inversely associated. The prevalence increased with age, and was lower in those with post graduate education.

No significant differences were seen by alcohol intake, physical activity levels, vitamin usage, or fruit intake. There was actually an

inverse relationship between vegetable intake (not fruit) and serum carotenoids.

Those who consumed 4 serves or more of vegetable were less likely to have the metabolic syndrome

compared to those who consumed 1 serve or less of vegetables.

The mean concentrations of serum alpha-carotene, beta-carotene and the sum of the five carotenoids were significantly lower for participants

with the metabolic syndrome present compared with those without the syndrome, after adjusting for potential confounding variables.

Concentrations of alpha-carotene, beta-carotene and the sum of the five carotenoids decreased significantly as

the number of components of the metabolic syndrome increased after adjusting for potential confounding variables.

Similarly there was an inverse association between quartiles of

individual and total serum carotenoids and metabolic syndrome status and each of its components.

This study was designed to investigate the association between several serum carotenoids and the metabolic syndrome.

The data from the present population study suggest that several serum carotenoids are inversely related to the metabolic syndrome.

The study showed significantly lower concentrations present among those with the metabolic syndrome of

α-carotene,
β-carotene and
the sum of the five carotenoids

compared to those without.We also found decreasing concentrations of all the carotenoids tested as

the number of the metabolic syndrome components increased.

This was significant for

α-carotene,
β-carotene,
β-cryptoxanthin
total carotenoids.
(not lycopenes)

These findings are consistent with data reported from the third National Health and Nutrition Examination Survey (NHANES III).

In the NHANES III study, significantly lower concentrations of all the carotenoids, except lycopene, were found among persons

with the metabolic syndrome compared with those without, after adjusting for confounding factors similar to those in our study.

Carnitine: A novel health factor-An overview.

CD Dayanand, N Krishnamurthy, S Ashakiran, KN Shashidhar

Int J Pharm Biomed Res 2011; 2(2): 79-89. ISSN No: 0976-0350

Carnitine comprises L-carnitine, acetyl –L-carnitine and Propionyl –L-carnitine. Carnitine is

obtained in greater amount from animal dietary sources than from plant sources.

The endogenous synthesis of carnitine takes place in animal tissues like

liver
kidney
brain

using precursor amino acids lysine and methionine by a pathway

dependent on iron, vitamin C, niacin, pyridoxine .

This is the basis of vegans generally depending on carnitine in larger proportion

through in vivo synthesis than omnivorous subjects.

The concentration of tri-methyl lysine residues and the tissue specificity of butyro-betaine dehydrogenase

plays a significant role in regulating the carnitine biosynthesis.

Carnitine transport from the site of synthesis to target tissue occurs via blood.

The measurement of plasma carnitine concentration represents –

the balance between the rate of synthesis and rate of excretion
- through specific transporter proteins.

The cellular functional role of carnitine depends on the uptake into cells through

carnitine transport proteins and
transport into mitochondrial matrix.

The function of carnitine is to traverse Long-chain Fatty Acids across inner mitochondrial membrane

for β-oxidation, thereby, generating ATP.

Carnitine deficiency results in muscle disorders. The deficiency states are primary and secondar.

The primary is of systemic or myopathic, characterized by a defect of high affinity organic cation transporter protein (CTP)

present on the plasma membrane of liver and kidney and
also due to dysfunction of carnitine reabsorbtion through
- similar transport proteins in renal tubules.

Secondary carnitine deficiency is associated with

mitochondrial disorders and also
defective β-oxidation such as CPT-II and acyl CoA dehydrogenase.

In recent times, carnitine has been extensively studied in various research activities to explore the therapeutic benefit.

Thus, carnitine justifies as a novel health factor.

http://pharmsicdirect.com/2011/Carnitine-A_novel_health_factor-An_overview/

Propionyl-L-carnitine Corrects Metabolic and Cardiovascular Alterations in
Diet-Induced Obese Mice and Improves Liver Respiratory Chain Activity

C Mingorance, L Duluc, M Chalopin, G Simard, et al.

http://PLoSOne.org/article/info:doi/10.1371/journal.pone.0034268

PLC improved the insulin-resistant state and reversed the increased total cholesterol
but not the increase in free fatty acid, triglyceride and HDL/LDL ratio induced by high-fat diet.
Vehicle-HF exhibited a reduced

cardiac output/body weight ratio,
endothelial dysfunction and
tissue decrease of NO production,

all of them being improved by PLC treatment.
The decrease of hepatic mitochondrial activity by high-fat diet was reversed by PLC.

Oral administration of PLC improves the insulin-resistant state developed by obese animals and
decreases the cardiovascular risk associated with the metabolically impaired mitochondrial function.

Omega-3 Fatty Acid and cardioprotection

The Benefits of Flaxseed

By Elaine Magee, MPH, RD WebMD Expert Column
Some call it one of the most powerful plant foods on the planet. There’s some evidence it may help reduce your risk of

heart disease, cancer, stroke, and diabetes.

That’s quite a tall order for a tiny seed that’s been around for centuries.

Flaxseed was cultivated in Babylon as early as 3000 BC. In the 8th century, King Charlemagne believed so strongly in the
health benefits of flaxseed that he passed laws requiring his subjects to consume it. Now, thirteen centuries later, some
experts say we have preliminary research to back up what Charlemagne suspected.

http://img.webmd.com/dtmcms/live/webmd/consumer_assets/site_images/article_
thumbnails/features/benefits_of_flaxseed_features/375x321_benefits_of_flaxseed_features.jpg
Not only has consumer demand for flaxseed grown, agricultural use has also increased.
Flaxseed is what’s used to feed all those chickens that are laying eggs with higher levels of omega-3 fatty acids.
Although flaxseed contains all sorts of healthy components, it owes its primary healthy reputation to three of them:

Omega-3 essential fatty acids, have been shown to have heart-healthy effects. 1.8 grams of plant omega-3s/tablespoon ground.
Lignans, which have both plant estrogen and antioxidant qualities. 75 to 800 times more lignans than other plant foods.
Fiber. Flaxseed contains both the soluble and insoluble types.

Omega-3 Polyunsaturated Fatty Acids and Cardiovascular Diseases

CJ Lavie, RV Milani, MR Mehra, and HO Ventura.

J. Am. Coll. Cardiol. 2009;54;585-594. http://dx.doi.org/10.1016/j.jacc.2009.02.084

http://content.onlinejacc.org/cgi/content/full/54/7/585

Fish oil is obtained in the human diet by eating oily fish, such as

herring, mackerel, salmon, albacore tuna, and sardines, or
by consuming fish oil supplements or cod liver oil.

Fish do not naturally produce these oils, but obtain them through the ocean food chain from the marine microorganisms

that are the original source of the omega-3 polyunsaturated fatty acids (ω-3 PUFA) found in fish oils.

Numerous prospective and retrospective trials from many countries, including the U.S., have shown that moderate

fish oil consumption decreases the risk of major cardiovascular (CV) events, such as

myocardial infarction (MI),
sudden cardiac death (SCD),
coronary heart disease (CHD),
atrial fibrillation (AF), and most recently,
death in patients with heart failure (HF).

Most of the evidence for benefits of the ω-3 PUFA has been obtained for

eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), the long-chain fatty acids in this family.

There is support for a benefit from alpha-linolenic acid (ALA),

the plant-based precursor of EPA.

The American Heart Association (AHA) has currently endorsed the use of ω-3 PUFA in patients with documented CHD

at a dose of approximately 1 g/day of combined DHA and EPA, either in the form of fatty fish or fish oil supplements

The health benefits of these long chain fatty acids are numerous and remain an active area of research.

Omega-3 polyunsaturated fatty acid (ω-3 PUFA) therapy continues to show great promise in primary and,

particularly in secondary prevention of cardiovascular (CV) diseases.

This portion of discussion summarizes the current scientific data on the effects of the long chain ω-3 PUFA

in the primary and secondary prevention of various CV disorders.

The most compelling evidence for CV benefits of ω-3 PUFA comes from 4 controlled trials

of nearly 40,000 participants randomized to receive eicosapentaenoic acid (EPA)
with or without docosahexaenoic acid (DHA) in studies of patients
- in primary prevention,
- after myocardial infarction, and
- with heart failure (HF).

The evidence from retrospective epidemiologic studies and from large randomized controlled trials

show the benefits of ω-3 PUFA, specifically EPA and DHA, in primary and secondary CV prevention

and provide insight into potential mechanisms of these observed benefits.

Background Epidemiologic Evidence

During the past 3 decades, numerous epidemiologic and observational studies have been published on the CV benefits of ω-3 PUFA.

As early as 1944, Sinclair described the rarity of CHD in Greenland Eskimos, who consumed a diet high in whale, seal, and fish.

More than 30 years ago, Bang and Dyberg reported that despite a diet low in fruit, vegetables, and complex carbohydrates but

high in saturated fat and cholesterol, serum cholesterol and triglycerides were lower in Greenland Inuit than in age-matched residents

of Denmark, and the risk of MI was markedly lower in the Greenland population compared with the Danes. These initial observations raised

speculation on the potential benefits of ω-3 PUFA (particularly EPA and DHA) as the protective “Eskimo factor”.

Potential EPA and DHA Effects

Antiarrhythmic effects
Improvements in autonomic function
Decreased platelet aggregation
Vasodilation
Decreased blood pressure
Anti-inflammatory effects
Improvements in endothelial function
Plaque stabilization
Reduced atherosclerosis
Reduced free fatty acids and triglycerides
Up-regulated adiponectin synthesis
Reduced collagen deposition

The target EPA + DHA consumption should be at least 500 mg/day for individuals without underlying overt CV disease

and at least 800 to 1,000 mg/day for individuals with known coronary heart disease and HF.

Further studies are needed to determine optimal dosing and the relative ratio of DHA and EPA ω-3 PUFA that

provides maximal cardioprotection in those at risk of CV disease
as well in the treatment of atherosclerotic, arrhythmic, and primary myocardial disorders.

Lavie et al. Omega-3 PUFA and CV Diseases J Am Coll Cardiol 2009; 54(7): 585–94

Assessing Appropriateness of Lipid Management Among Patients With Diabetes Mellitus

Moving From Target to Treatment. AJ Beard, TP Hofer, JR Downs, et al. and Diabetes Clinical Action Measures Workgroup

Performance measures that emphasize only a treat-to-target approach may motivate ove-rtreatment with high-dose statins,

potentially leading to adverse events and unnecessary costs.

We developed a clinical action performance measure for lipid management in patients with diabetes mellitus that is designed

to encourage appropriate treatment with moderate-dose statins while minimizing over-treatment.

We examined data from July 2010 to June 2011 for 964 818 active Veterans Affairs primary care patients ≥18 years of age with diabetes mellitus.

We defined 3 conditions as successfully meeting the clinical action measure for patients 50 to 75 years old:

having a low-density lipoprotein (LDL) <100 mg/dL,
taking a moderate-dose statin regardless of LDL level or measurement, or
receiving appropriate clinical action (starting, switching, or intensifying statin therapy) if LDL is ≥100 mg/dL.

We examined possible over-treatment for patients ≥18 years of age by examining the proportion of patients

without ischemic heart disease who were on a high-dose statin.

We then examined variability in measure attainment across 881 facilities using 2-level hierarchical multivariable logistic models.

Of 668 209 patients with diabetes mellitus who were 50 to 75 years of age, 84.6% passed the clinical action measure:

67.2% with LDL <100 mg/dL,
13.0% with LDL ≥100 mg/dL and either on a moderate-dose statin (7.5%) or with appropriate clinical action (5.5%), and
4.4% with no index LDL on at least a moderate-dose statin. Of the entire cohort ≥18 years of age, 13.7% were potentially over-treated.

Use of a performance measure that credits appropriate clinical action indicates that almost 85% of diabetic veterans 50 to 75 years of age

are receiving appropriate dyslipidemia management.

Exercise training and mitochondria in heart failure

The beneﬁcial effects of exercise in the rehabilitation of patients with heart failure are well established,

with improvements observed in

exercise capacity,
quality of life,
hospitalization rates and
morbidity/mortality.

There is no evidence of training-induced

improvements in cardiac energy metabolism or

mitochondrial function, and
no modiﬁcation of myocardial oxidative capacity,
oxidative enzymes, or
energy transfer enzymes

in exercising rats with experimental heart failure, but there is evidence of

ventricular remodelling,
restored contractile function and
improved intracellular calcium handling.

There are also improvements in

skeletal muscle oxidative capacity with
increased mitochondrial density

following endurance training in heart failure patients associated with alleviation of symptoms such as

exercise intolerance and
chronic fatigue.

The mechanism underlying improvements in mitochondrial function may perhaps be a result of

more effective peripheral oxygen delivery following training,
alleviating tissue hypoxia and oxidative stress.

Treating Type 2 diabetes, and lowering cardiovascular disease risk

Treating Diabetes and Obesity with an FGF21-Mimetic Antibody
Activating the βKlotho/FGFR1c Receptor Complex

IN Foltz, S Hu, C King, Xinle Wu, et al. Amgen and Texas A&M HSC, Houston, TX.
Sci Transl Med Nov 2012; 4(162), p. 162ra153
http://dx.doi.org/10.1126/scitranslmed.3004690

Fibroblast growth factor 21 (FGF21) is a distinctive member of the FGF family with potent beneficial effects on

lipid
body weight
glucose metabolism

A monoclonal antibody, mimAb1, binds to βKlotho with high affinity and specifically

activates signaling from the βKlotho/FGFR1c (FGF receptor 1c) receptor complex.

Injection of mimAb1 into obese cynomolgus monkeys led to FGF21-like metabolic effects:

decreases in body weight,
plasma insulin,
triglycerides, and
glucose during tolerance testing.

Mice with adipose-selective FGFR1 knockout were refractory to FGF21-induced improvements

in glucose metabolism and body weight.

mimAb1 depends on βKlotho to activate FGFR1c, but

it is not expected to induce side effects caused by activating FGFR1c alone.

The results in obese monkeys (with mimAb1) and in FGFR1 knockout mice (with FGF21) demonstrated

the essential role of FGFR1c in FGF21 function and
suggest fat as a critical target tissue for the cytokine and antibody.

This antibody activates FGF21-like signaling through cell surface receptors, and provided

preclinical validation for an innovative therapeutic approach to diabetes and obesity.

Influencing Factors on Cardiac Structure and Function Beyond Glycemic Control
in Patients With Type 2 Diabetes Mellitus (T2DM)

R Ichikawa, M Daimon, T Miyazaki, T Kawata, et al. Cardiovasc Diabetol. 2013;12(38)

We studied 148 asymptomatic patients with T2DM without overt heart disease.
Early (E) and late (A) diastolic mitral flow velocity and early diastolic mitral annular velocity (e’)

were measured for assessing left ventricular (LV) diastolic function.

In addition

insulin resistance,
non-esterified fatty acid,
high-sensitive CRP,
estimated glomerular filtration rate,
waist/hip ratio,
abdominal visceral adipose tissue (VAT),
subcutaneous adipose tissue (SAT)

In T2DM (compared to controls),

E/A and e’ were significantly lower, and
E/e’, left atrial volume and LV mass were significantly greater

VAT and age were independent determinants of

left atrial volume (β =0.203, p=0.011),
E/A (β =−0.208, p=0.002), e’ (β =−0.354, p<0.001) and
E/e’ (β=0.220, p=0.003).

Independent determinants of LV mass were

systolic blood pressure,
waist-hip ratio (β=0.173, p=0.024)
VAT/SAT ratio (β=0.162, p=0.049)

Excessive visceral fat accompanied by adipocyte dysfunction may play a greater role than

glycemic control in the development of diastolic dysfunction and LV hypertrophy in T2DM

Inhibition of oxidative stress and mtDNA damage

Novel pharmacological agents are needed that

optimize substrate metabolism and
maintain mitochondrial integrity,
improve oxidative capacity in heart and skeletal muscle, and
alleviate many of the clinical symptoms associated with heart failure.

The evidence for the attenuation or loss of effectiveness of neurohormonal antagonism as heart failure worsens

indicates future therapeutic targets must address the cellular and molecular mechanisms that contribute to heart failure.

Pharmacological Targets of oxidative stress and mitochondrial damage

Defective mitochondrial energetics and abnormal substrate metabolism are fundamental characteristics of CHF.

A significant beneﬁt may be derived from developing therapies aimed at

preserving cardiac mitochondrial function and
optimizing substrate metabolism.

Oxidative stress is enhanced in myocardial remodelling and failure. The increased production of oxygen radicals in the failing heart

with preserved antioxidant enzyme activities suggests
mitochondrial electron transport as a source of oxygen radical generation
can be a therapeutic target against oxidant-induced damage in the failing myocardium.

Chronic increases in oxygen radical production in the mitochondria

leads to mitochondrial DNA (mtDNA) damage,
functional decline,
further oxygen radical generation, and
cellular injury.

MtDNA defects may thus play an important role in the

development and progression of myocardial remodelling and failure.

Reactive oxygen species induce

myocyte hypertrophy,
apoptosis, and
interstitial fibrosis
by activating matrix metallo-proteinases,
promoting the development and
progression of maladaptive myocardial remodelling and failure.

http://cardiovascres.oxfordjournals.org/content/81/3/449/F1.small.gif

Oxidative stress has direct effects on cellular structure and function and

may activate integral signalling molecules in myocardial remodelling and failure (Figure).

ROS result in a phenotype characterized by

hypertrophy and apoptosis in isolated cardiac myocytes.

http://cardiovascres.oxfordjournals.org/content/81/3/449/F2.small.gif

Therefore, oxidative stress and mtDNA damage are good therapeutic targets.

Overexpression of the genes for

peroxiredoxin-3 (Prx-3), a mitochondrial antioxidant, or
mitochondrial transcription factor A (TFAM),
- could ameliorate the decline in mtDNA copy number in failing hearts.

Consistent with alterations in mtDNA, the

decrease in mitochondrial function was prevented,
proving that the activation of Prx-3 or TFAM gene expression
could ameliorate the pathophysiological processes seen

in mitochondrial dysfunction and
myocardial remodelling.

Inhibition of oxidative stress and mtDNA damage

could be novel and effective treatment strategies for heart failure.

http://cardiovascres.oxfordjournals.org/content/81/3/449/F3.small.gif

Proposed mechanisms through which overexpression of the

mitochondrial transcription factor A (TFAM) gene prevents
mitochondrial DNA (mtDNA) damage,
oxidative stress, and
myocardial remodelling and failure.

In wild-type mice, mitochondrial transcription factor A

directly interacts with mitochondrial DNA to form nucleoids.

Stress such as ischaemia causes mitochondrial DNA damage, which

increases the production of reactive oxygen species (ROS)
leading to a catastrophic cycle of mitochondrial electron transport impairment,
further reactive oxygen species generation, and mitochondrial dysfunction.

TFAM overexpression may protect mitochondrial DNA from damage by

directly binding and stabilizing mitochondrial DNA and
increasing the steady-state levels of mitochondrial DNA

ameliorating mitochondrial dysfunction and thus the development and progression of heart failure.

Conclusion

Heart failure is a multifactorial syndrome that is characterized by

abnormal energetics and substrate metabolism in heart and skeletal muscle.

Although existing therapies have been beneﬁcial, there is a clear need for new approaches to treatment.

Pharmacological targeting of the cellular stresses underlying mitochondrial dysfunction, such as

elevated fatty acid levels,
tissue hypoxia and oxidative stress and
metabolic modulation of heart and skeletal muscle mitochondria,
- appears to offer a promising therapeutic strategy for tackling heart failure.

Murray AJ, Anderson RE, Watson GC, et al. Uncoupling proteins in human heart. Lancet 2004; 364:1786.

Delarue J, Magnan C. Free fatty acids and insulin resistance. Curr Opin ClinNutr Metab Care 2007; 10:142

Lee L, Campbell R, Scheuermann-Freestone M, et al. Metabolic modulation with perhexiline in chronic heart failure: a randomized, controlled trialof short-term use of a novel treatment. Circulation 2005; 112:3280

Tsutsui H, Kinugawa S, Matsushima S. Mitochondrial oxidative stress and dysfunction in myocardial remodelling. Cardiovasc Res. 2009;81(3):449-56. http://dxdoi.org/10.1093/cvr/cvn280.

C Maack, M Böhm. Targeting Mitochondrial Oxidative Stress in Heart Failure. J Am Coll Cardiol. 2011;58(1):83-86. http://dx.doi.org/10.1016/j.jacc.2011.01.032

http://content.onlinejacc.org/article.aspx?articleid=1146578

References

Mitochondrial dynamics and cardiovascular diseases Ritu Saxena
http://pharmaceuticalintelligence.com/2012/11/14/mitochondrial-dynamics-and-cardiovascular-diseases/

Mitochondrial Damage and Repair under Oxidative Stress larryhbern
http://pharmaceuticalintelligence.com/2012/10/28/mitochondrial-damage-and-repair-under-oxidative-stress/

Mitochondria: Origin from oxygen free environment, role in aerobic glycolysis, metabolic adaptation larryhbern
http://pharmaceuticalintelligence.com/2012/09/26/mitochondria-origin-from-oxygen-free-environment-role-in-aerobic-glycolysis-metabolic-adaptation/

Ca2+ signaling: transcriptional control larryhbern
http://pharmaceuticalintelligence.com/2013/03/06/ca2-signaling-transcriptional-control/

MIT Scientists on Proteomics: All the Proteins in the Mitochondrial Matrix identified Aviva Lev-Ari
http://pharmaceuticalintelligence.com/2013/02/03/mit-scientists-on-proteomics-all-the-proteins-in-the-mitochondrial-matrix-identified/

Nitric Oxide has a ubiquitous role in the regulation of glycolysis -with a concomitant influence on mitochondrial function larryhbern
http://pharmaceuticalintelligence.com/2012/09/16/nitric-oxide-has-a-ubiquitous-role-in-the-regulation-of-glycolysis-with-a-concomitant-influence-on-mitochondrial-function/

Ubiquinin-Proteosome pathway, autophagy, the mitochondrion, proteolysis and cell apoptosis larryhbern
http://pharmaceuticalintelligence.com/2013/02/14/ubiquinin-proteosome-pathway-autophagy-the-mitochondrion-proteolysis-and-cell-apoptosis-reconsidered/

Low Bioavailability of Nitric Oxide due to Misbalance in Cell Free Hemoglobin in Sickle Cell Disease – A Computational Model Anamika Sarkar
http://pharmaceuticalintelligence.com/2012/11/09/low-bioavailability-of-nitric-oxide-due-to-misbalance-in-cell-free-hemoglobin-in-sickle-cell-disease-a-computational-model/

The rationale and use of inhaled NO in Pulmonary Artery Hypertension and Right Sided Heart Failure larryhbern
http://pharmaceuticalintelligence.com/2012/08/20/the-rationale-and-use-of-inhaled-no-in-pulmonary-artery-hypertension-and-right-sided-heart-failure/

Mitochondria and Cardiovascular Disease: A Tribute to Richard Bing, Larry H Bernstein, MD, FACP
http://pharmaceuticalintelligence.com/2013/04/14/chapter-5-mitochondria-and-cardiovascular-disease/

Mitochondrial Metabolism and Cardiac Function, Larry H Bernstein, MD, FACP
http://pharmaceuticalintelligence.com/2013/04/14/mitochondrial-metabolism-and-cardiac-function/

Mitochondrial Dysfunction and Cardiac Disorders, Larry H Bernstein, MD, FACP
http://pharmaceuticalintelligence.com/2013/04/14/mitochondrial-dysfunction-and-cardiac-disorders/

Reversal of Cardiac mitochondrial dysfunction, Larry H Bernstein, MD, FACP
http://pharmaceuticalintelligence.com/2013/04/14/reversal-of-cardiac-mitochondrial-dysfunction/

Clinical Trials Results for Endothelin System: Pathophysiological role in Chronic Heart Failure, Acute Coronary Syndromes and MI – Marker of Disease Severity or Genetic Determination? Aviva Lev-Ari, PhD, RN 10/19/2012
http://pharmaceuticalintelligence.com/2012/10/19/clinical-trials-results-for-endothelin-system-pathophysiological-role-in-chronic-heart-failure-acute-coronary-syndromes-and-mi-marker-of-disease-severity-or-genetic-determination/

Endothelin Receptors in Cardiovascular Diseases: The Role of eNOS Stimulation, Aviva Lev-Ari, PhD, RN 10/4/2012
http://pharmaceuticalintelligence.com/2012/10/04/endothelin-receptors-in-cardiovascular-diseases-the-role-of-enos-stimulation/

Inhibition of ET-1, ETA and ETA-ETB, Induction of NO production, stimulation of eNOS and Treatment Regime with PPAR-gamma agonists (TZD): cEPCs Endogenous Augmentation for Cardiovascular Risk Reduction – A Bibliography, Aviva Lev-Ari, PhD, RN 10/4/2012
http://pharmaceuticalintelligence.com/2012/10/04/inhibition-of-et-1-eta-and-eta-etb-induction-of-no-production-and-stimulation-of-enos-and-treatment-regime-with-ppar-gamma-agonists-tzd-cepcs-endogenous-augmentation-for-cardiovascular-risk-reduc/

Genomics & Genetics of Cardiovascular Disease Diagnoses: A Literature Survey of AHA’s Circulation Cardiovascular Genetics, 3/2010 – 3/2013, L H Bernstein, MD, FACP and Aviva Lev-Ari,PhD, RN 3/7/2013
http://pharmaceuticalintelligence.com/2013/03/07/genomics-genetics-of-cardiovascular-disease-diagnoses-a-literature-survey-of-ahas-circulation-cardiovascular-genetics-32010-32013/

Cardiovascular Disease (CVD) and the Role of agent alternatives in endothelial Nitric Oxide Synthase (eNOS) Activation and Nitric Oxide Production, Aviva Lev-Ari, PhD, RN 7/19/2012 http://pharmaceuticalintelligence.com/2012/07/19/cardiovascular-disease-cvd-and-the-role-of-agent-alternatives-in-endothelial-nitric-oxide-synthase-enos-activation-and-nitric-oxide-production/

Cardiovascular Risk Inflammatory Marker: Risk Assessment for Coronary Heart Disease and Ischemic Stroke – Atherosclerosis. Aviva Lev-Ari, PhD, RN 10/30/2012
http://pharmaceuticalintelligence.com/2012/10/30/cardiovascular-risk-inflammatory-marker-risk-assessment-for-coronary-heart-disease-and-ischemic-stroke-atherosclerosis/

Cholesteryl Ester Transfer Protein (CETP) Inhibitor: Potential of Anacetrapib to treat Atherosclerosis and CAD. Aviva Lev-Ari, PhD, RN 4/7/2013
http://pharmaceuticalintelligence.com/2013/04/07/cholesteryl-ester-transfer-protein-cetp-inhibitor-potential-of-anacetrapib-to-treat-atherosclerosis-and-cad/

Hypertriglyceridemia concurrent Hyperlipidemia: Vertical Density Gradient Ultracentrifugation a Better Test to Prevent Undertreatment of High-Risk Cardiac Patients, Aviva Lev-Ari, PhD, RN 4/4/2013 http://pharmaceuticalintelligence.com/2013/04/04/hypertriglyceridemia-concurrent-hyperlipidemia-vertical-density-gradient-ultracentrifugation-a-better-test-to-prevent-undertreatment-of-high-risk-cardiac-patients/

Fight against Atherosclerotic Cardiovascular Disease: A Biologics not a Small Molecule – Recombinant Human lecithin-cholesterol acyltransferase (rhLCAT) attracted AstraZeneca to acquire AlphaCore.
Aviva Lev-Ari, PhD, RN 4/3/2013
http://pharmaceuticalintelligence.com/2013/04/03/fight-against-atherosclerotic-cardiovascular-disease-a-biologics-not-a-small-molecule-recombinant-human-lecithin-cholesterol-acyltransferase-rhlcat-attracted-astrazeneca-to-acquire-alphacore/

High-Density Lipoprotein (HDL): An Independent Predictor of Endothelial Function & Atherosclerosis, A Modulator, An Agonist, A Biomarker for Cardiovascular Risk. Aviva Lev-Ari, PhD, RN 3/31/2013
http://pharmaceuticalintelligence.com/2013/03/31/high-density-lipoprotein-hdl-an-independent-predictor-of-endothelial-function-artherosclerosis-a-modulator-an-agonist-a-biomarker-for-cardiovascular-risk/

Peroxisome proliferator-activated receptor (PPAR-gamma) Receptors Activation: PPARγ transrepression for Angiogenesis in Cardiovascular Disease and PPARγ transactivation for Treatment of Diabetes.
Aviva Lev-Ari, PhD, RN 11/13/2012
http://pharmaceuticalintelligence.com/2012/11/13/peroxisome-proliferator-activated-receptor-ppar-gamma-receptors-activation-pparγ-transrepression-for-angiogenesis-in-cardiovascular-disease-and-pparγ-transactivation-for-treatment-of-dia/

Sulfur-Deficiciency and Hyperhomocysteinemia, L H Bernstein, MD, FACP
http://pharmaceuticalintelligence.com/2013/04/04/sulfur-deficiency-and-hyperhomocusteinemia/

Sulfur-Deficiciency and Hyperhomocysteinemia (pharmaceuticalintelligence.com)
Mitochondrial metabolism and cardiac function (pharmaceuticalintelligence.com)
Macrophage Migration Inhibitory Factor Inhibition Is Deleterious for High-Fat Diet-Induced Cardiac Dysfunction (plosone.org)
L-carnitine significantly improves patient outcomes following heart attack (eurekalert.org)
Mitochondrial Disorders Overview (geneticamedicala.wordpress.com)
An Appraisal of Human Mitochondrial DNA Instability: New Insights into the Role of Non-Canonical DNA Structures and Sequence Motifs (plosone.org)
Cardiotoxicity and Cardiomyopathy Related to Drugs Adverse Effects (pharmaceuticalintelligence.com)
Lp(a) Gene Variant Association (pharmaceuticalintelligence.com)
Mitochondrial dysfunction and cardiac disorders (pharmaceuticalintelligence.com)
Reversal of cardiac mitochondrial dysfunction (pharmaceuticalintelligence.com)

Structure of the human mitochondrial genome. (Photo credit: Wikipedia)

English: Treatment Guidelines for Chronic Heart Failure (Photo credit: Wikipedia)

English: Oxidative stress process Italiano: Processo dello stress ossidativo (Photo credit: Wikipedia)

Diagram taken from the paper “Dissection of mitochondrial superhaplogroup H using coding region SNPs” (Photo credit: Asparagirl)

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In Focus: Targeting of Cancer Stem Cells

Posted in Bio Instrumentation in Experimental Life Sciences Research, CANCER BIOLOGY & Innovations in Cancer Therapy, Pharmacotherapy and Cell Activity, Stem Cells for Regenerative Medicine, tagged ABC, ABCC1, ABCG2, anti-cancer therapy, antiapoptosis, Bcl-2, biomarkers, cancer stem cells, CD133, chemoresistance, DNA damage, DNA repair, efflux transporter, glioblastoma multiforme, Glioma, Imatinib, Interleukin 6, LSCs, MDR1, Multi-drug resistance, Non-small cell lung cancer, radiotherapy resistance, self-renewal, stem cells, TGFβ, tumors, Wnt/β catenin, xeno transplantation model on March 27, 2013| 9 Comments »

Author and Curator: Ritu Saxena, Ph.D

Although cancer stem cells constitute only a small percentage of the tumor burden, their self-renewal capacity and possible link with recurrence of cancer post treatment makes them a sought after therapeutic target in cancer. The post on cancer stem cells published on the 22^nd of March, 2013, describes the identity of CSCs, their functional characteristics, possible cell of origin and biomarkers. This post focuses on the therapeutic potential of CSCs, their resistance to conventional anti-tumor therapies and current therapeutic targets including biomarkers, signaling pathways and niches.

CSCs Are Resistant to conventional anticancer therapies including chemotherapy, radiotherapy and surgery that are used either alone or in combination. However, these strategies have failed several times to eradicate CSCs resulting in metastasis and relapse, hence, a fatal disease outcome.

The properties of CSCs that contribute to or lead to chemoresistance include:

Quiescent Phenotype

Chemotherapeutic agents target fast-growing cells; however, some CSCs that remain in the dormant or quiescent stage are spared from lethal damage. Later, when the dormant CSCs enter cell cycle, tumor proliferation is stimulated.

Antiapoptosis

Antiapoptotic proteins such as BCL-2 and some self-renewal pathways such as transforming growth factor β, Wnt/ β -catenin or BMI-1 are activated in CSCs. Consequently, DNA damage repair capability of CSCs is enhanced after genotoxic stress or activation of autocrine loops through the production of growth factors like epidermal growth factor (Moserle L, Cancer Lett, 1 Feb 2010;288(1):1-9).

Expression of Drug Efflux Pumps

CSCs express some proteins that have typically been known to contribute to multidrug resistance. The proteins are drug efflux pumps ABCC1, ABCG2 or MDR1. Multidrug resistance-associated proteins (ABCC subfamily) are members of the ATP-binding cassette (ABC) superfamily of transport proteins and act as cellular efflux transporters for a wide variety of substrates, in particular glutathione, glucuronide and sulfate conjugates of diverse compounds.

Radiotherapy is mainly used in breast cancer and glioblastoma multiforme. In glioblastoma multiforme, the properties of CSCs that contribute to radiotherapy resistance is the presence of CD133 marker. CD133+ CSCs preferentially activate DNA damage repair pathway and significantly induced checkpoint kinases that leads to reduced apoptosis in CSCs compared to the CD133- tumor cells (Bao S, Nature, 7 Dec 2006;444(7120):756-60).

Radiotherapy resistance in breast cancer is due to reduced levels of reactive oxygen species in CSCs. In addition, radiation resistance of progenitor cells in an immortalized breast cancer cell line was mediated by the Wnt/β catenin pathway proteins (Diehn M, et al, Nature, 9 Apr 2009;458(7239):780-3; Chen MS, et al, J Cell Sci, 1 Feb 2007;120(Pt 3):468-77).

As mentioned in the previous post on CSCs, CSC targeting therapy could either eliminate CSCs by either killing them after differentiating them from other tumor population, and/or by disrupting their niche. Efficient eradication of CSCs may require the combined ablation of CSCs themselves and their niches. Thus, identification of appropriate and specific markers of CSCs is crucial for targeting them and preventing tumor relapse. Table 1 (adapted from a review article on CSCs by Zhao et al) describes the currently used biomarkers for CSC-targeted therapy (Zhao L, et al, Eur Surg Res, 2012;49(1):8-15).

Table 1

Specific Target	Cancer type	Marker properties and therapy
*Targeting cell markers*
CD24+CD44+ESA+	Pancreatic cancer	Pancreatic CSCs, elevated during tumorigenesis
CD44+CD24–ESA+	Breast cancer	Breast CSCs
EpCAM high CD44+CD166+	Colorectal cancer
CD34+CD38–	AML	broad use as a target for chemotherapy
CD133+	Prostate cancer and breast cancer	5-transmembrane domain cell surface glycoprotein,also a marker for neuron epithelial, hematopoietic and endothelialprogenitor cells
Stro1+CD105+CD44+	Bone sarcoma
Nodal/activin		Knockdown or pharmacological inhibition of its receptorAlk4/7 abrogated self-renewal capacity and in vivo tumorigenicity of CSCs.
*Targeting signaling pathways*
Hedgehog signaling	Upregulated in several cancer types	inhibitors: GDC-0449,PF04449913, BMS-833923, IPI-926 and TAK-441
Wnt/β-catenin signaling	CML, squamous cell carcinoma	Be required for CSC self-renewal and tumor growthinhibitors: PRI-724, WIF-1 and telomerase
Notch signaling	Several cancer types	An important regulator in normal development, adult stem cell maintenance,and tumorigenesis in multiple organs,inhibitors: RO4929097, BMS-906024, IPI-926 and MK0752
PI3K/Akt/PTEN/mTOR,	Several cancer types	The pathway is deregulated in many tumors and used to preferentially target CSCsinhibitors: temsirolimus, everolimus FDA-approved therapy for renal cell carcinoma
*Targeting CSC Niche*
Angiogenesis Niche	Colon cancer, breast cancer, NSCLC	Inhibitor: bevacizumab results in a disruption of the CSC niche, depleted vasculature and a dramatic reduction in the number of CSCs.
Hypoxia (HIF pathway)	Ovarian cancer, lung cancer, cervical cancer	Inhibitors: topotecan and digoxin have been approved for ovarian, lung and cervical cancer
Targeting Micro RNA
miR-200 family		Inhibits EMT and cancer cell migration by direct targeting of E-cadherin transcriptional repressors ZEB1 and ZEB2
Let-7 family		Regulates BT-IC stem cell-like properties by silencing more than one target
miR-124		Related to neuronal differentiation, targets laminin γ1 and integrin β1.
miR-21		Suppresses the self-renewal of embryonic stem cells

The challenge is to develop an effective treatment regimen that prevents survival, self-renewal and differentiation of CSCs and also disturbs their niche without damaging normal stem cells. In order to evaluate the efficiency of CSC-targeting therapies, in vitro models and mouse xenotransplantation models have been used for preclinical studies. Some potential CSC targeting agents in preclinical stages include notch inhibitors for glioblastoma stem cells and telomerase peptide vaccination after chemoradiotherapy of non-small cell lung cancer stem cells Stem Cells (Hovinga KE, et al, Jun 2010;28(6):1019-29; Serrano D, Mol Cancer, 9 Aug 2011;10:96). In addition, several phase II and phase III trials are currently underway to test CSC-targeting drugs focusing on efficacy and safety of treatment.

Reference:

Bao S, Nature, 7 Dec 2006;444(7120):756-60).

Diehn M, et al, Nature, 9 Apr 2009;458(7239):780-3

Chen MS, et al, J Cell Sci, 1 Feb 2007;120(Pt 3):468-77

Zhao L, et al, Eur Surg Res, 2012;49(1):8-15

Hovinga KE, et al, Jun 2010;28(6):1019-29

Serrano D, Mol Cancer, 9 Aug 2011;10:96

Pharmaceutical Intelligence posts:

http://pharmaceuticalintelligence.com/2013/03/22/in-focus-identity-of-cancer-stem-cells/ Author and curator: Ritu Saxena, PhD

http://pharmaceuticalintelligence.com/2012/08/15/to-die-or-not-to-die-time-and-order-of-combination-drugs-for-triple-negative-breast-cancer-cells-a-systems-level-analysis/ Authors: Anamika Sarkar, PhD and Ritu Saxena, PhD

http://pharmaceuticalintelligence.com/2013/03/07/the-importance-of-cancer-prevention-programs-new-perceptions-for-fighting-cancer/ Author: Ziv Raviv, PhD

http://pharmaceuticalintelligence.com/2013/03/03/treatment-for-metastatic-her2-breast-cancer/ Reporter: Larry H Bernstein, MD

http://pharmaceuticalintelligence.com/2013/03/02/recurrence-risk-for-breast-cancer/ Larry H Bernstein, MD

http://pharmaceuticalintelligence.com/2013/02/14/prostate-cancer-androgen-driven-pathomechanism-in-early-onset-forms-of-the-disease/ Curator: Aviva Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2013/01/15/exploring-the-role-of-vitamin-c-in-cancer-therapy/ Curator: Ritu Saxena, PhD

http://pharmaceuticalintelligence.com/2013/01/12/harnessing-personalized-medicine-for-cancer-management-prospects-of-prevention-and-cure-opinions-of-cancer-scientific-leaders-httppharmaceuticalintelligence-com/ Curator: Aviva Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2013/01/10/the-molecular-pathology-of-breast-cancer-progression/ Author and reporter: Tilda Barliya PhD

http://pharmaceuticalintelligence.com/2012/11/30/histone-deacetylase-inhibitors-induce-epithelial-to-mesenchymal-transition-in-prostate-cancer-cells/ Reporter and Curator: Stephen J. Williams, PhD

http://pharmaceuticalintelligence.com/2012/10/22/blood-vessel-generating-stem-cells-discovered/ Reporter: Ritu Saxena, PhD

http://pharmaceuticalintelligence.com/2012/10/17/stomach-cancer-subtypes-methylation-based-identified-by-singapore-led-team/ Reporter: Aviva Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2012/09/17/natural-agents-for-prostate-cancer-bone-metastasis-treatment/ Reporter: Ritu Saxena, PhD

http://pharmaceuticalintelligence.com/2012/08/28/cardiovascular-outcomes-function-of-circulating-endothelial-progenitor-cells-cepcs-exploring-pharmaco-therapy-targeted-at-endogenous-augmentation-of-cepcs/ Aviva Lev-Ari, PhD, RN

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In focus: Triple Negative Breast Cancer

Posted in Biological Networks, Gene Regulation and Evolution, Biomarkers & Medical Diagnostics, CANCER BIOLOGY & Innovations in Cancer Therapy, Cell Biology, Signaling & Cell Circuits, Genome Biology, Genomic Testing: Methodology for Diagnosis, Molecular Genetics & Pharmaceutical, Personalized and Precision Medicine & Genomic Research, tagged breast cancer, Cancer - General, cell cycle, Chemotherapy, clonal cells, clonal heterogeneity, DNA repair, gene expression, HMEC, molecular subtyping, Myc, neoadjuvant chemotherapy, PI3K, Ras, Ras/MAPK, residual disease, SABCS, SABCS 2012, San Antonio Breast Cancer Symposium, shRNA, Therapy, TNBC, Triple-negative breast cancer on January 29, 2013| 3 Comments »

Latest research efforts reported in the San Antonio Breast Cancer Symposium, 2012

Curator: Ritu Saxena, Ph.D.

‘Triple negative breast cancer’ or TNBC, as the name suggests, is a classification of breast cancers lacking the expression of estrogen receptor (ER) and progesterone receptor expression as well as amplification of the human epidermal growth factor receptor 2 (HER2).

Unlike other breast cancer types, treating TNBC is a challenge mainly because of the absence of well-defined molecular targets and because of disease heterogeneity. Currently, neoadjuvant chemotherapies are in use to treat TNBC patients. Some, around 30%, patients respond completely to neoadjuvant chemotherapy and have good outcomes after surgery. However, if there is a residual disease after therapy, outcomes are poor.

Therefore, current focus of the field is to first understand the complexity of the disease, both at genomic and molecular level and look for targets. Also, several combination chemotherapies are currently under trial to determine the efficacy, overall response rate, progression-free survival and other relevant factors for patients suffering with different forms of TNBC.

Recently, in the San Antonio Breast Cancer Symposium (SABCS 2012), several abstarcts related to TNBC research, both clinical and pre-clinical. Here is a compilation of some of the abstracts and their relevance in the field of TNBC research:

Triple Negative Breast Cancer: Subtypes, Molecular Targets, and Therapeutic Approaches, Pietenpol JA, Vanderbilt-Ingram Cancer Center; Vanderbilt University School of Medicine (Nashville, TN), Abstract no. ES2-2.

In order to better understand the complexity of TNBC, an integrative and comprehensive genomic and molecular analysis is required. The analysis would give important cues to developing and administering effective therapeutic agents. The group has compiled an extensive number of TNBC gene expression profiles and initiated molecular subtyping of the disease. Differential GE was used to designate 25 TNBC cell line models representative of the following subtypes:

two basel-like TNBC subtypes with cell cycle and DDR gene expression signatures (BL1 and BL2);
two mesenchymal subtypes with high expression of genes involved in differentiation and growth factor pathways (M and MSL);
an immunomodulatory (IM) type;
a luminal subtype driven by androgen signaling (LAR)

The pharmacological drugs were chosen on the basis of the genetic pathways active in the cell lines with the abovementioned TNBC subtypes. It was observed that BL1 and BL2 subtype cell lines respond to cisplatin. Mesenchymal, basal, and luminal subtype lines with aberrations in PI3K signaling and have the greatest sensitivity to PI3K inhibitors.

The LAR subtype cell lines express AR and are uniquely sensitive to bicalutamide (AR antagonist). The experiment was a proof-of-concept that the best therapy could be based on TNBC subtypes.

The group has also developed a web-based subtyping tool referred to as “TNBCtype,” for candidate TNBC tumor samples using our gene expression metadata and classification methods. The approach would enable alignment of TNBC patients to appropriate targeted therapies.

The Clonal and Mutational Composition of Triple Negative Breast Cancers: Aparicio S, University of British Columbia (Vancouver, BC), Canada. Abstract no. ES2-3.

The abstract is on the same lines, TNBC heterogeneity that is. The concept of clonal heterogeneity in cancers, the spatial and temporal variation in clonal composition, is the focal point of the discussion. The group has developed next generation sequencing approaches and applied them to the understanding of mutational and clonal composition of primary TNBC. They have demonstrated that both mutational composition and clonal structure of primary TNBC is in fact a complete spectrum, a notion that is far from the previous one that stated TNBC to be a distinct disease. The authors add “clonal analysis suggests a means by which the genetic complexity might be reduced by following patient evolution over time and space.” The specific implications of the mutational and transcriptome landscapes of TNBC in relation to possible disease biologies were discussed in the symposium.

Profiling of triple-negative breast cancers after neoadjuvant chemotherapy identifies targetable molecular alterations in the treatment-refractory residual disease:

Balko JM, etal, Vanderbilt University (Nashville, TN); Foundation Medicine, (Cambridge, MA); Instituto Nacional de Enfermedades Neoplásicas, Lima, Peru

In the absence of hormone receptors and hence lack of targets, Neoadjuvant chemotherapy (NAC) is increasingly used in patients with TNBC. NAC can induce a pathologic complete response (pCR) in ∼30% of patients which portends a favorable prognosis. In contrast, patients with residual disease (RD) in the breast at surgical resection exhibit worse outcomes. The authors hypothesize that “profiling residual TNBC after NAC would identify molecularly targetable lesions in the chemotherapy resistant component of the tumor and that the persistent tumor cells would mirror micro-metastases which ultimately recur in such patients.” The researchers utilized targeted next generation sequencing (NGS) for 182 oncogenes and tumor suppressors in a CLIA certified lab (Foundation Medicine, Cambridge, MA) and gene expression profiling (NanoString) of the RD after NAC in 102 patients with TNBC. The RD was stained for Ki67, which has been reported to predict outcome after NAC in unselected breast cancers. Out of the 89 evaluable post-NAC tumors, 57 (64%) were basal-like; 19% HER2-enriched; 6% luminal A; 6% luminal B and 5% normal-like. Of 81 tumors evaluated by NGS, 89% demonstrated mutations in TP53, 27% were MCL1-amplified, and 21% were MYC-amplified.

Several pathways were found to be altered:

PI3K/mTOR pathway (AKT1-3, PIK3CA, PIK3R1, RAPTOR, PTEN, and TSC1)
Cell cycle genes (amplifications of CDK2, CDK4, and CDK6, CCND1-3, and CCNE1); loss of RB
DNA repair pathway (BRCA1/2, ATM)
Ras/MAPK pathway (KRAS, RAF1, NF1)
Sporadic growth factor receptor (amplifications occurred in EGFR, KIT, PDGFRA, PDGFRB, MET, FGFR1, FGFR2, and IGF1R.

NGS identified 7 patients with ERBB2 gene amplification. NGS could assist in the identification of ERBB2-overexpressing tumors misclassified at the time of diagnosis.

Amplifications of MYC were independently associated with poor recurrence-free survival (RFS) and overall survival (OS). In contrast to the earlier notion, high post-NAC Ki67 score did not predict poor RFS or OS in this predominantly TNBC cohort.

The authors concluded that “the diversity of lesions in residual TNBCs after NAC underscores the need for powerful and broad molecular approaches to identify actionable molecular alterations and, in turn, better inform personalized therapy of this aggressive disease.”

Identification of Novel Synthetic-Lethal Targets for MYC-Driven Triple-Negative Breast Cancer: Goga A, etal, UCSF (San Francisco, CA), Abstract No. S3-8

Reiterating the greatest challenge of the TNBC treatment, no targeted agents currently exist against TNBC. The group at UCSF has discovered that TNBC frequently express high levels of the MYC proto-oncogene. The discovery has led them to identify new “synthetic-lethal” strategies to selectively kill TNBC with MYC overexpression. “Synthetic lethality arises when a combination of mutations in two or more genes leads to cell death, whereas a mutation in only one of these genes has little effect. Using this strategy, we can take advantage of the elevated MYC signaling in TNBC to selectively kill them, while sparing normal tissues in which MYC is expressed at much lower levels”

The researchers performed a shRNA synthetic-lethal screen in the human mammary epithelial cells (HMEC), to identify new molecules, such as cell cycle kinases, which when inhibited can preferentially kill TNBC cells. A high-throughput screen of ∼2000 shRNAs, that target the human kinome (∼ 600 kinases) when performed, led to the identification of 13 kinases whose inhibition by >1 shRNAs gave rise to >50% inhibition of cell growth. ARK5 and GSK3A were the two other kinases that were shown to have a synthetic-lethal interaction with MYC. Since these two kinases have been identified in other studies, it gives validity to the ability to the methods of Goga etal in identifying synthetic-lethal targets. The group is currently characterizing and validating the 11 novel targets identified in this screen, using human cancer cell lines as well as mouse cancer models to determine the impact of inhibiting these targets on triple-negative breast cancer development and proliferation.

Reference:

Dent R, etal. Triple-negative breast cancer: clinical features and patterns of recurrence (2007) Clin Cancer Res 13, 4429-4434.

Lehmann BD, etal. Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies (2011) J Clin Invest. 121: 2750-67.

Chen X, etal. TNBCtype: A Subtyping Tool for Triple- Negative Breast Cancer. (2012) Cancer informatics 11, 147-156.

Abstracts presented in SABCS 2012 can be accessed here.

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Posts Tagged ‘DNA repair’

New Topoisomerase Inhibitors in Clinical Trials

From a 2015 Clinical Cancer Research paper:

Abstract

AND From ASCO 2015 Annual Meeting

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Good and Bad News Reported for Ovarian Cancer Therapy

However FDA investigators voiced their skepticism of AstraZeneca’s clinical results, namely

This was certainly a disappointment as ….

PARP1 Inhibitors Currently in Clinical Trials for Ovarian Cancer

Summary of Combination Ovarian Cancer Trials with Avastin (current and closed)

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Good and Bad News Reported for Ovarian Cancer Therapy

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Cancer Mutations Across the Landscape

UPDATED 4/24/2020 The genomic landscape of pediatric cancers: Curation of WES/WGS studies shows need for more data

Mutational landscape and significance across 12 major cancer types

Introduction

Standardization of mutation data

Distinct mutation frequencies and sequence context

Significantly mutated genes

Common mutations

Figure 5 | Driver initiation and progression mutations and tumour clonal mutation is in the subclone

Survival Analysis

Driver mutations and tumour clonal architecture

References (20 of 38)

UPDATED 4/24/2020 The genomic landscape of pediatric cancers: Curation of WES/WGS studies shows need for more data

Somatic alterations in pediatric cancers

Genome landscape studies

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Nrf2 as a novel molecular target for chemoprevention.

Abstract

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Mitochondrial metabolism and cardiac function

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Substrate metabolism in the failing heart

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Lipoic Acid & Acetyl-L-Carnitine

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Other Mitochondrial Antioxidants

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Metabolic syndrome and serum carotenoids.

Carnitine: A novel health factor-An overview.

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Omega-3 Fatty Acid and cardioprotection The Benefits of Flaxseed

Omega-3 Polyunsaturated Fatty Acids and Cardiovascular Diseases

Background Epidemiologic Evidence

Assessing Appropriateness of Lipid Management Among Patients With Diabetes Mellitus

Exercise training and mitochondria in heart failure

Treating Type 2 diabetes, and lowering cardiovascular disease risk

Treating Diabetes and Obesity with an FGF21-Mimetic Antibody Activating the βKlotho/FGFR1c Receptor Complex

Influencing Factors on Cardiac Structure and Function Beyond Glycemic Control in Patients With Type 2 Diabetes Mellitus (T2DM)

Inhibition of oxidative stress and mtDNA damage

Pharmacological Targets of oxidative stress and mitochondrial damage

Conclusion

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Metabolic syndrome and serum carotenoids: findings of a cross-sectional study
in Queensland, Australia

Propionyl-L-carnitine Corrects Metabolic and Cardiovascular Alterations in
Diet-Induced Obese Mice and Improves Liver Respiratory Chain Activity

Omega-3 Fatty Acid and cardioprotection

The Benefits of Flaxseed

Treating Diabetes and Obesity with an FGF21-Mimetic Antibody
Activating the βKlotho/FGFR1c Receptor Complex

Influencing Factors on Cardiac Structure and Function Beyond Glycemic Control
in Patients With Type 2 Diabetes Mellitus (T2DM)