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1.  A Predictive Genetic Signature for Response to Fluoropyrimidine-Based Neoadjuvant Chemoradiation in Clinical Stage II and III Rectal Cancer 
Frontiers in Oncology  2013;3:288.
Purpose: Pre-operative chemoradiation (CRT) is currently the standard of care for patients with clinical stage II and III rectal cancer but only about 45% of patients achieve tumor downstaging and <20% of patients achieve a pathologic complete response. Better methods to stratify patients according to potential neoadjuvant treatment response are needed. We used microarray analysis to identify a genetic signature that correlates with a pathological complete response (pCR) to neoadjuvant CRT. We performed a gene network analysis to identify potential signaling pathways involved in determining response to neoadjuvant treatment.
Patients and Methods: We identified 31 T3–4 N0–1 rectal cancer patients who were treated with neoadjuvant fluorouracil-based CRT. Eight patients were identified to have achieved a pCR to treatment while 23 patients did not. mRNA expression was analyzed using cDNA microarrays. The correlation between mRNA expression and pCR from pre-treatment tumor biopsies was determined. Gene network analysis was performed for the genes represented by the predictive signature.
Results: A genetic signature represented by expression levels of the three genes EHBP1, STAT1, and GAPDH was found to correlate with a pCR to neoadjuvant treatment. The difference in expression levels between patients who achieved a pCR and those who did not was greatest for EHBP1. Gene network analysis showed that the three genes can be connected by the gene ubiquitin C (UBC).
Conclusion: This study identifies a 3-gene signature expressed in pre-treatment tumor biopsies that correlates with a pCR to neoadjuvant CRT in patients with clinical stage II and III rectal cancer. These three genes can be connected by the gene UBC, suggesting that ubiquitination is a molecular mechanism involved in determining response to treatment. Validating this genetic signature in a larger number of patients is proposed.
PMCID: PMC3839295  PMID: 24324931
rectal neoplasms; ubiquitination; gene array; UBC; EHBP1
2.  BNIP3 is Essential for Mediating 6-thioguanine-and 5-fluorouracil-induced Autophagy Following DNA Mismatch Repair Processing 
Cell research  2010;20(6):665-675.
DNA mismatch repair (MMR) processes the chemically-induced mispairs following treatment with clinically important nucleoside analogs such as 6-thioguanine (6-TG) and 5-fluorouracil (5-FU). MMR processing of these drugs has been implicated in activation of a prolonged G2/M cell cycle arrest for repair and later induction of apoptosis and/or autophagy for irreparable DNA damage. In this study, we investigated the role of BNIP3 in the activation of autophagy and the temporal relationship between a G2/M cell cycle arrest and the activation of BNIP3-mediated autophagy following MMR processing of 6-TG and 5-FU. We found that BNIP3 protein levels are up-regulated in a MLH1 (MMR+)-dependent manner following 6-TG and 5-FU treatment. Subsequent siRNA-mediated BNIP3 knockdown abrogates 6-TG -induced autophagy. We also found that p53 knockdown or inhibition of mTOR activity by rapamycin cotreatment impairs 6-TG and 5-FU-induced up-regulation of BNIP3 protein levels and autophagy. Furthermore, suppression of Chk1 expression and a subsequent reduction in 6-TG-induced G2/M cell cycle arrest by Chk1 siRNA promotes the extent of 6-TG-induced autophagy. These findings suggest that BNIP3 mediates 6-TG- and 5-FU induced autophagy in a p53- and mTOR-dependent manner. Additionally, the duration of Chk1-activated G2/M cell cycle arrest determines the level of autophagy following MMR processing of these nucleoside analogs.
PMCID: PMC3430372  PMID: 20368736
BNIP3; p53; mTOR; autophagy; nucleoside analogs
3.  Quantitative Analysis of the Effects of Iododeoxyuridine and Ionizing Radiation Treatment on the Cell Cycle Dynamics of DNA Mismatch Repair Deficient Human Colorectal Cancer Cells 
IET systems biology  2013;7(4):10.1049/iet-syb.2012.0050.
DNA mismatch repair (MMR) is involved in processing DNA damage following treatment with ionizing radiation (IR) and various classes of chemotherapy drugs including iododeoxyuridine (IUdR), a known radiosensitizer. In this study, we have developed asynchronous probabilistic cell cycle models to assess the isolated effects of IUdR and IR and the combined effects of IUdR+IR treatments on MMR damage processing. We used both synchronous and asynchronous MMR-proficient/MMR-deficient cell populations and followed treated cells for up to 2 cell cycle times. We have observed and quantified differential cell cycle responses to MMR damage processing following IR and IUdR+IR treatments, principally in the duration of both G1 and G2/M cell cycle phases. The models presented in this work form the foundation for the development of an approach to maximize the therapeutic index for IR and IUdR+IR treatments in MMR-deficient (damage tolerant) cancers.
PMCID: PMC3884822  PMID: 23919954
DNA mismatch repair; cell cycle; Iododeoxyuridine; ionizing radiation; colon cancer; mathematical modelling
4.  Developing an In Silico Model of the Modulation of Base Excision Repair using Methoxyamine for More Targeted Cancer Therapeutics 
IET systems biology  2013;7(2):27-37.
Base Excision Repair (BER) is a major DNA repair pathway involved in the processing of exogenous nonbulky base damages from certain classes of cancer chemotherapy drugs as well as ionizing radiation. Methoxyamine (MX) is a small molecule chemical inhibitor of BER that is shown to enhance chemotherapy and/or ionizing radiation cytotoxicity in human cancers. In this paper, we have analysed the inhibitory effect of MX on the base excision repair pathway kinetics using a computational model of the repair pathway. The inhibitory effect of MX depends on the base excision repair efficiency. We have generated variable efficiency groups using different sets of protein concentrations generated by Latin hypercube sampling, and we have clustered simulation results into high, medium and low efficiency repair groups. From analysis of the inhibitory effect of MX on each of the three groups, it is found that the inhibition is most effective for high efficiency base excision repair, and least effective for low efficiency repair.
PMCID: PMC3884826  PMID: 23847811
Base excision repair; dynamical modelling; therapeutic gain; cancer treatment
5.  Integration of Principles of Systems Biology and Radiation Biology: Toward Development of in silico Models to Optimize IUdR-Mediated Radiosensitization of DNA Mismatch Repair Deficient (Damage Tolerant) Human Cancers 
Over the last 7 years, we have focused our experimental and computational research efforts on improving our understanding of the biochemical, molecular, and cellular processing of iododeoxyuridine (IUdR) and ionizing radiation (IR) induced DNA base damage by DNA mismatch repair (MMR). These coordinated research efforts, sponsored by the National Cancer Institute Integrative Cancer Biology Program (ICBP), brought together system scientists with expertise in engineering, mathematics, and complex systems theory and translational cancer researchers with expertise in radiation biology. Our overall goal was to begin to develop computational models of IUdR- and/or IR-induced base damage processing by MMR that may provide new clinical strategies to optimize IUdR-mediated radiosensitization in MMR deficient (MMR−) “damage tolerant” human cancers. Using multiple scales of experimental testing, ranging from purified protein systems to in vitro (cellular) and to in vivo (human tumor xenografts in athymic mice) models, we have begun to integrate and interpolate these experimental data with hybrid stochastic biochemical models of MMR damage processing and probabilistic cell cycle regulation models through a systems biology approach. In this article, we highlight the results and current status of our integration of radiation biology approaches and computational modeling to enhance IUdR-mediated radiosensitization in MMR− damage tolerant cancers.
PMCID: PMC3355906  PMID: 22649757
mismatch repair; ionizing radiation; iododeoxyuridine; systems biology
6.  Ribonucleotide Reductase Inhibitors: A New Look at an Old Target for Radiosensitization 
Ribonucleotide reductase (RR), the rate limiting enzyme in the synthesis and repair of DNA, has been studied as a target for inhibition in the treatment of cancer for many years. While some researchers have focused on RR inhibitors as chemotherapeutic agents, particularly in hematologic malignancies, some of the most promising data has been generated in the field of radiosensitization. Early pre-clinical studies demonstrated that the addition of the first of these drugs, hydroxyurea, to ionizing radiation (IR) produced a synergistic effect in vitro, leading to a large number of clinical studies in the 1970–1980s. These studies, mainly in cervical cancer, initially produced a great deal of interest, leading to the incorporation of hydroxyurea in the treatment protocols of many institutions. However, over time, the conclusions from these studies have been called into question and hydroxyurea has been replaced in the standard of care of cervical cancer. Over the last 10 years, a number of well-done pre-clinical studies have greatly advanced our understanding of RR as a target. Those advances include the elucidation of the role of p53R2 and our understanding of the temporal relationship between the delivery of IR and the response of RR. At the same time, new inhibitors with increased potency and improved binding characteristics have been discovered, and pre-clinical and early clinical data look promising. Here we present a comprehensive review of the pre-clinical and clinical data in the field to date and provide some discussion of future areas of research.
PMCID: PMC3356024  PMID: 22655252
ribonucleotide reductase; hydroxyurea; triapine; radiosensitizer; ionizing radiation; cervical cancer
7.  A Rapid, Simple DNA Mismatch Repair Substrate Construction Method 
A more flexible and higher-yielding in vitro DNA mismatch repair (MMR) substrate construction method, which was developed initially by Wang and Hays, is described for the construction of a nucleotide-based chemical mismatch (G/IU) and a G/T mismatch. Our modifications use the combination of two endonuclease enzymes (NheI and BciVI) and two new redesigned plasmids (pWDAH1A and pWDSH1B). In our modified methodology, plasmids are initially digested with the nicking endonucleases, followed by the streptavidin treatment. The mismatch-containing oligo is then annealed to the gap DNA and finally ligated to produce a mismatch-containing DNA substrate. We report a high efficiency (up to 90%) of these mismatch substrates and confirm recognition using a functional assay. These modifications, coupled with the use of the redesigned plasmids, can be applied for the construction of other types of chemically induced mismatches as well as insertion-deletion loops for future in vitro studies of MMR processing by our group and others.
PMCID: PMC3356146  PMID: 22655228
mismatch repair; mismatch substrates construction; iododeoxyuridine
8.  Differential cellular responses to prolonged low dose rate ionizing radiation in MLH1-proficient and -deficient colorectal cancer HCT116 cells 
MLH1 is a key DNA mismatch repair (MMR) protein involved in maintaining genomic stability by participating in the repair of endogenous and exogenous mispairs in the daughter strands during S-phase. Exogenous mispairs can result following treatment with several classes of chemotherapeutic drugs as well as with ionizing radiation (IR). In this study, we investigated the role of the MLH1 protein in determining the cellular and molecular responses to prolonged low dose rate (LDR) IR, which is similar to the clinical use of cancer brachytherapy.
Experimental design
An isogenic pair of MMR+ (MLH1+) and MMR− (MLH1−) human colorectal cancer HCT116 cells were exposed to prolonged LDR-IR (1.3–17cGy/h × 24–96 h). The clonogenic survival and gene mutation rates were examined. Cell cycle distribution was analyzed with flow cytometry. Changes in selected DNA damage repair proteins, DNA damage response proteins and cell death marker proteins were examined with Western blotting.
MLH1+ HCT116 cells showed greater radiosensitivity with enhanced expression of apoptotic and autophagic markers; a reduced HPRT gene mutation rate; and more pronounced cell cycle alterations (increased late S population and a G2/M arrest) following LDR-IR compared to MLH1− HCT116 cells. Importantly, a progressive increase in MLH1 protein levels was found in MLH1+ cells during prolonged LDR-IR, which was temporally correlated with a progressive decrease in Rad51 protein (involved in homologous recombination, HR) levels.
MLH1 status significantly affects cellular responses to prolonged LDR-IR. MLH1 may enhance cell radiosensitivity to prolonged LDR-IR through inhibition of HR (via inhibition of Rad51).
PMCID: PMC2783277  PMID: 19861440
mismatch repair; low dose rate IR; MLH1; Rad51; late S phase
9.  Essential role of DNA base excision repair on survival in an acidic tumor microenvironment 
Cancer research  2009;69(18):7285-7293.
The base excision repair (BER) pathway is required to repair endogenous and exogenous oxidative DNA damage. Multiple DNA repair pathways have been shown to be down-regulated in the tumor microenvironment, whereas APE1/Ref1, a central protein in BER, is overexpressed in many types of solid tumors. APE1/Ref1 has dual functions, participating both in BER and in redox regulation of oxidized transcription factors. Here, we show that inhibition of the BER pathway in an acidic tumor microenvironment increases oxidative DNA damage temporally related to increased intracellular reactive oxygen species. Unrepaired oxidative DNA damage results in cell cycle arrests and increased DNA double strand breaks, leading to cell death. Therefore, up-regulation of BER in solid cancers may represent an adaptive survival response. Consequently, BER inhibition may confer tumor microenvironment targeted cytotoxicity in human cancers. Our data suggest that BER inhibition is a rational basis for cancer therapy with or without other cytotoxic therapy. Additionally, our results offer insight as to why APE1/Ref1 retains it’s unique dual functionality, both of which counteract environmental oxidative stress.
PMCID: PMC2745500  PMID: 19723658
base excision repair; APE1/Ref1; XRCC1; tumor microenvironment; DNA damage
10.  Analysis of Cell Cycle Dynamics using Probabilistic Cell Cycle Models 
In this study, we develop asynchronous probabilistic cell cycle models to quantitatively assess the effect of ionizing radiation on a human colon cancer cell line. We use both synchronous and asynchronous cell populations and follow treated cells for up to 2 cell cycle times. The model outputs quantify the changes in cell cycle dynamics following ionizing radiation treatment, principally in the duration of both G1 and G2/M phases.
PMCID: PMC3884824  PMID: 22254270
11.  Radiation Therapy in Addition to Gross Total Resection of Retroperitoneal Sarcoma Results in Prolonged Survival: Results from a Single Institutional Study 
Journal of Oncology  2009;2008:824036.
Purpose. Typical treatment of retroperitoneal sarcomas (RPSs) is surgery with or without radiation therapy for localized disease. With surgery alone, local failure rates are as high as 90%; this led to radiation therapy playing an important role in the treatment of RPSs. Methods. Thirty-one patients with retroperitoneal sarcoma treated with gross total resection and radiation therapy make up this retrospective analysis. Nineteen were treated preoperatively and 12 postoperatively (median dose, 59.4 Gy)—sixteen also received intraoperative radiation therapy (IORT) (median dose, 11 Gy). Patients were followed with stringent regimens, including frequent CT scans of the chest, abdomen, and pelvis. Results. With a median follow-up of 19 months (range 1–66 months), the 2-year overall survival (OS) rate is 70% (median, 52 months). The 2-year locoregional control (LRC) rate is 77% (median, 61.6 months). The 2-year distant disease free survival (DDFS) rate is 70% (median not reached). There were no differences in radiation-related acute and late toxicities among patients treated pre- versus postoperatively, whether with or without IORT. Conclusions. Compared to surgery alone, neoadjuvant or adjuvant radiation therapy offers patients with RPS an excellent chance for long-term LRC, DDS, and OS. The integration of modern treatment planning for external beam radiation therapy and IORT allows for higher doses to be delivered with acceptable toxicities.
PMCID: PMC2648636  PMID: 19277103
12.  Adjuvant Therapy for Rectal Cancer 
Patients with stage II and III rectal cancer benefit from a multidisciplinary approach to treatment. Studies of postoperative adjuvant therapy consistently demonstrate decreases in locoregional recurrence with the use of radiation therapy. The use of postoperative chemotherapy results in improved disease-free survival and overall survival in certain studies. Preoperative radiation therapy decreases locoregional recurrence and in one study demonstrated an improvement in survival. The addition of chemotherapy to preoperative radiation results in improved locoregional control, but not survival. Preoperative chemoradiation is the standard of care for patients with clinical stage II and III rectal cancer in the United States due to improved local recurrence, acute and late toxicity, and sphincter preservation compared with postoperative chemoradiation. Promising approaches include the incorporation of new chemotherapeutic and biologic agents into chemoradiation and adjuvant chemotherapy regimens; new radiation techniques, such as the use of intraoperative radiation therapy and an accelerated concomitant radiation boost; and gene and protein expression profiling, to better predict response to treatment and prognosis.
PMCID: PMC2789506  PMID: 20011198
Rectal cancer; radiation; chemotherapy; adjuvant; review
13.  5-iodo-2-pyrimidinone-2′-deoxyribose (IPdR)-mediated cytotoxicity and radiosensitization in U87 human glioblastoma xenografts 
5-iodo-2-pyrimidinone-2′-deoxyribose (IPdR) is a novel orally administered (po) prodrug of 5-iododeoxyuridine (IUdR). As po IPdR is being considered for clinical testing as a radiosensitizer in patients with high grade gliomas, we performed this in vivo study of IPdR-mediated cytotoxicity and radiosensitization in a human glioblastoma xenograft model, U87.
Methods and Materials
Groups of 8–9 athymic male nude mice (6–8 weeks old) were implanted with sc U87 xenograft tumors (4 × 106 cells) and then randomized to 10 treatment groups receiving increasing doses of po IPdR (0, 100, 250, 500, and 1000 mg/kg/d) administered once daily (qd) × 14 d with or without radiation therapy (RT) (0 or 2 Gy/d × 4 d) on days 11–14 of IPdR treatment. Systemic toxicity was determined by body weight measurements during and following IPdR treatment. Tumor response was assessed by changes in tumor volumes.
IPdR alone at doses of ≥500 mg/kg/d results in moderate inhibition of tumor growth. The combination of IPdR + RT results in a significant IPdR dose-dependent tumor growth delay with the maximum radiosensitization using ≥500 mg/kg/d. IPdR doses of 500 and 1000 mg/kg/d did result in transient 5–15% body weight loss during treatment.
In U87 human glioblastoma sc xenografts, po IPdR given qd × 14 d and RT given 2 Gy/d × 4 d (days 11–14 of IPdR treatment) results in a significant tumor growth delay in an IPdR dose-dependent pattern. The use of po IPdR + RT holds promise for phase I/II testing in patients with high grade gliomas.
PMCID: PMC2128756  PMID: 17967315
IpdR; U87 xenografts; radiosensitization
14.  Ribonucleotide Reductase Inhibition Enhances Chemoradiosensitivity of Human Cervical Cancers 
Radiation research  2010;174(5):574-581.
For repair of damaged DNA, cells increase de novo synthesis of deoxyribonucleotide triphosphates through the rate-limiting, p53-regulated ribonucleotide reductase (RNR) enzyme. In this study we investigated whether pharmacological inhibition of RNR by 3-aminopyridine-2-carboxaldehyde thiosemicarbazone (3-AP, NSC #663249) enhanced chemoradiation sensitivity through a mechanism involving sustained DNA damage. RNR inactivation by 3-AP and resulting chemoradiosensitization were evaluated in human cervical (CaSki, C33-a) cancer cells through study of DNA damage (γ-H2AX signal) by flow cytometry, RNR subunit p53R2 and p21 protein steady-state levels by Western blot analysis and laser scanning imaging cytometry, and cell survival by colony formation assays. 3-AP treatment led to sustained radiation- and cisplatin-induced DNA damage (i.e. increased γ-H2AX signal) in both cell lines through a mechanism of inhibited RNR activity. Radiation, cisplatin and 3-AP exposure resulted in significantly elevated numbers and persistence of γ-H2AX foci that were associated with reduced clonogenic survival. DNA damage was associated with a rise in p53R2 but not p21 protein levels 6 h after treatment with radiation and/or cisplatin plus 3-AP. We conclude that blockage of RNR activity by 3-AP impairs DNA damage responses that rely on deoxyribonucleotide production and thereby may substantially increase chemoradiosensitivity of human cervical cancer.
PMCID: PMC3529744  PMID: 20954859
15.  Phase I trial of pelvic radiation, weekly cisplatin, and 3-aminopyridine-2-carboxaldehyde thiosemicarbazone (3-AP, NSC #663249) for locally advanced cervical cancer 
This study assessed the safety/tolerability, pharmacokinetics, and clinical activity of three-times weekly intravenous 3-aminopyridine-2-carboxaldehyde thiosemicarbazone (3-AP, NSC #663249) in combination with once weekly intravenous cisplatin and daily pelvic radiation in patients with gynecologic malignancies. 3-AP is a novel small molecule inhibitor of ribonucleotide reductase (RNR) and is being tested as a potential radiosensitizer and chemosensitizer.
Experimental Design
Patients with stage IB2-IVB cervical cancer (n=10) or recurrent uterine sarcoma (n=1) were assigned to dose-finding cohorts of 2-hour 3-AP infusions during five weeks of cisplatin chemoradiation. Pharmacokinetic and methemoglobin samples and tumor biopsy for RNR activity were obtained on days 1 and 10. Clinical response was assessed.
The maximum tolerated 3-AP dose is 25mg/m2 given three-times weekly during cisplatin and pelvic radiation. Two patients experienced manageable 3-AP-related grade 3 or 4 electrolyte abnormalities. 3-AP pharmacokinetics showed a 2-hour half-life, with median peak plasma concentrations of 277ng/mL (25mg/m2) and 467ng/mL (50mg/m2). Median methemoglobin levels peaked at 1% (25mg/m2) and 6% (50mg/m2) at 4 hours after initiating 3-AP infusions. No change in RNR activity was found on day 1 versus 10 in six early complete responders, while elevated RNR activity was seen on day 10 as compared to day 1 in four late complete responders (P =0.02). Ten (100%) patients with stage IB2-IVB cervical cancer achieved complete clinical response and remain without disease relapse with a median 18 months of follow-up (6-32 months).
3-AP was well tolerated at a three-times weekly intravenous 25mg/m2 dose during cisplatin and pelvic radiation.
PMCID: PMC2822897  PMID: 20145183
Triapine; cervical cancer; ribonucleotide reductase; radiosensitization
16.  Modulating Radiation Resistance by Inhibiting Ribonucleotide Reductase in Cancers with Virally or Mutationally Silenced p53 Protein 
Radiation research  2009;172(6):666.
Therapeutic ionizing radiation damages DNA, increasing p53-regulated ribonucleotide reductase (RNR) activity required for de novo synthesis of the deoxyribonucleotide triphosphates used during DNA repair. This study investigated the pharmacological inhibition of RNR in cells of virally or mutationally silenced p53 cancer cell lines using 3-aminopyridine-2-carboxaldehyde thiosemicarbazone (3-AP, Triapine® NSC #663249), a chemotherapeutic radiosensitizer that equally inhibits RNR M2 and p53R2 small subunits. The effects of 3-AP on RNR inhibition and resulting radiosensitization were evaluated in cervical (CaSki, HeLa and C33-a) and colon (RKO, RKO-E6) cancer cells. 3-AP treatment significantly enhanced radiation-related cytotoxicity in cervical and colon cancer cells. 3-AP treatment significantly decreased RNR activity, caused prolonged radiation-induced DNA damage, and resulted in an extended G1/S-phase cell cycle arrest in all cell lines. Similar effects were observed in both RKO and RKO-E6 cells, suggesting a p53-independent mechanism of radiosensitization. We conclude that inhibition of ribonucleotide reductase by 3-AP enhances radiation-mediated cytotoxicity independent of p53 regulation by impairing repair processes that rely on deoxyribonucleotide production, thereby substantially increasing the radiation sensitivity of human cancers.
PMCID: PMC2818576  PMID: 19929413
17.  Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes 
Klionsky, Daniel J. | Abeliovich, Hagai | Agostinis, Patrizia | Agrawal, Devendra K. | Aliev, Gjumrakch | Askew, David S. | Baba, Misuzu | Baehrecke, Eric H. | Bahr, Ben A. | Ballabio, Andrea | Bamber, Bruce A. | Bassham, Diane C. | Bergamini, Ettore | Bi, Xiaoning | Biard-Piechaczyk, Martine | Blum, Janice S. | Bredesen, Dale E. | Brodsky, Jeffrey L. | Brumell, John H. | Brunk, Ulf T. | Bursch, Wilfried | Camougrand, Nadine | Cebollero, Eduardo | Cecconi, Francesco | Chen, Yingyu | Chin, Lih-Shen | Choi, Augustine | Chu, Charleen T. | Chung, Jongkyeong | Clarke, Peter G.H. | Clark, Robert S.B. | Clarke, Steven G. | Clavé, Corinne | Cleveland, John L. | Codogno, Patrice | Colombo, María I. | Coto-Montes, Ana | Cregg, James M. | Cuervo, Ana Maria | Debnath, Jayanta | Demarchi, Francesca | Dennis, Patrick B. | Dennis, Phillip A. | Deretic, Vojo | Devenish, Rodney J. | Di Sano, Federica | Dice, J. Fred | DiFiglia, Marian | Dinesh-Kumar, Savithramma | Distelhorst, Clark W. | Djavaheri-Mergny, Mojgan | Dorsey, Frank C. | Dröge, Wulf | Dron, Michel | Dunn, William A. | Duszenko, Michael | Eissa, N. Tony | Elazar, Zvulun | Esclatine, Audrey | Eskelinen, Eeva-Liisa | Fésüs, László | Finley, Kim D. | Fuentes, José M. | Fueyo, Juan | Fujisaki, Kozo | Galliot, Brigitte | Gao, Fen-Biao | Gewirtz, David A. | Gibson, Spencer B. | Gohla, Antje | Goldberg, Alfred L. | Gonzalez, Ramon | González-Estévez, Cristina | Gorski, Sharon | Gottlieb, Roberta A. | Häussinger, Dieter | He, You-Wen | Heidenreich, Kim | Hill, Joseph A. | Høyer-Hansen, Maria | Hu, Xun | Huang, Wei-Pang | Iwasaki, Akiko | Jäättelä, Marja | Jackson, William T. | Jiang, Xuejun | Jin, Shengkan | Johansen, Terje | Jung, Jae U. | Kadowaki, Motoni | Kang, Chanhee | Kelekar, Ameeta | Kessel, David H. | Kiel, Jan A.K.W. | Kim, Hong Pyo | Kimchi, Adi | Kinsella, Timothy J. | Kiselyov, Kirill | Kitamoto, Katsuhiko | Knecht, Erwin | Komatsu, Masaaki | Kominami, Eiki | Kondo, Seiji | Kovács, Attila L. | Kroemer, Guido | Kuan, Chia-Yi | Kumar, Rakesh | Kundu, Mondira | Landry, Jacques | Laporte, Marianne | Le, Weidong | Lei, Huan-Yao | Lenardo, Michael J. | Levine, Beth | Lieberman, Andrew | Lim, Kah-Leong | Lin, Fu-Cheng | Liou, Willisa | Liu, Leroy F. | Lopez-Berestein, Gabriel | López-Otín, Carlos | Lu, Bo | Macleod, Kay F. | Malorni, Walter | Martinet, Wim | Matsuoka, Ken | Mautner, Josef | Meijer, Alfred J. | Meléndez, Alicia | Michels, Paul | Miotto, Giovanni | Mistiaen, Wilhelm P. | Mizushima, Noboru | Mograbi, Baharia | Monastyrska, Iryna | Moore, Michael N. | Moreira, Paula I. | Moriyasu, Yuji | Motyl, Tomasz | Münz, Christian | Murphy, Leon O. | Naqvi, Naweed I. | Neufeld, Thomas P. | Nishino, Ichizo | Nixon, Ralph A. | Noda, Takeshi | Nürnberg, Bernd | Ogawa, Michinaga | Oleinick, Nancy L. | Olsen, Laura J. | Ozpolat, Bulent | Paglin, Shoshana | Palmer, Glen E. | Papassideri, Issidora | Parkes, Miles | Perlmutter, David H. | Perry, George | Piacentini, Mauro | Pinkas-Kramarski, Ronit | Prescott, Mark | Proikas-Cezanne, Tassula | Raben, Nina | Rami, Abdelhaq | Reggiori, Fulvio | Rohrer, Bärbel | Rubinsztein, David C. | Ryan, Kevin M. | Sadoshima, Junichi | Sakagami, Hiroshi | Sakai, Yasuyoshi | Sandri, Marco | Sasakawa, Chihiro | Sass, Miklós | Schneider, Claudio | Seglen, Per O. | Seleverstov, Oleksandr | Settleman, Jeffrey | Shacka, John J. | Shapiro, Irving M. | Sibirny, Andrei | Silva-Zacarin, Elaine C.M. | Simon, Hans-Uwe | Simone, Cristiano | Simonsen, Anne | Smith, Mark A. | Spanel-Borowski, Katharina | Srinivas, Vickram | Steeves, Meredith | Stenmark, Harald | Stromhaug, Per E. | Subauste, Carlos S. | Sugimoto, Seiichiro | Sulzer, David | Suzuki, Toshihiko | Swanson, Michele S. | Tabas, Ira | Takeshita, Fumihiko | Talbot, Nicholas J. | Tallóczy, Zsolt | Tanaka, Keiji | Tanaka, Kozo | Tanida, Isei | Taylor, Graham S. | Taylor, J. Paul | Terman, Alexei | Tettamanti, Gianluca | Thompson, Craig B. | Thumm, Michael | Tolkovsky, Aviva M. | Tooze, Sharon A. | Truant, Ray | Tumanovska, Lesya V. | Uchiyama, Yasuo | Ueno, Takashi | Uzcátegui, Néstor L. | van der Klei, Ida | Vaquero, Eva C. | Vellai, Tibor | Vogel, Michael W. | Wang, Hong-Gang | Webster, Paul | Wiley, John W. | Xi, Zhijun | Xiao, Gutian | Yahalom, Joachim | Yang, Jin-Ming | Yap, George | Yin, Xiao-Ming | Yoshimori, Tamotsu | Yu, Li | Yue, Zhenyu | Yuzaki, Michisuke | Zabirnyk, Olga | Zheng, Xiaoxiang | Zhu, Xiongwei | Deter, Russell L.
Autophagy  2007;4(2):151-175.
Research in autophagy continues to accelerate,1 and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used for this purpose.2,3 There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi). Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes. This set of guidelines is not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to verify an autophagic response.
PMCID: PMC2654259  PMID: 18188003
autolysosome; autophagosome; flux; lysosome; phagophore; stress; vacuole

Results 1-17 (17)