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Posts Tagged ‘Proceedings of the National Academy of Sciences of the United States of America’


Cloning the Vaccinia Virus Genome as a Bacterial Artificial Chromosome

Curator: Larry H Bernstein, MD, FCAP

Cloning the vaccinia virus genome as a bacterial artificial chromosome in Escherichia coli and recovery of infectious virus in mammalian cells

A Domi and B Moss
PNAS  Sep 17, 2002; 99(19):12415–12420     http://www.pnas.org/dx.cgi.doi/10.1073/pnas.192420599
The ability to manipulate the vaccinia virus (VAC) genome,
  • as a plasmid in bacteria,
  • would greatly facilitate genetic studies and
  • provide a powerful alternative method of making recombinant viruses.
VAC, like other poxviruses, has a linear, double-stranded DNA genome with covalently closed hairpin ends that are resolved
  • from transient head-to-head and tail-to-tail concatemers
  • during replication in the cytoplasm of infected cell.
Our strategy to construct a nearly 200,000-bp VAC-bacterial artificial chromosome (BAC) was based on
  • circularization of head-to-tail concatemers of VAC DNA.
Cells were infected with a recombinant VAC containing inserted sequences for plasmid replication and maintenance in Escherichia coli; DNA concatemer resolution was inhibited
  • leading to formation and accumulation of head-to-tail concatemers,
in addition to the usual head-to-head and tail-to-tail forms;
  • the concatemers were circularized
    • by homologous or Cre–loxP-mediated recombination; and
  • E. coli were transformed with DNA from the infected cell lysates.
Stable plasmids containing the entire VAC genome, with an intact concatemer junction sequence, were identified. Rescue of infectious VAC was consistently achieved
  • by transfecting the VAC–BAC plasmids into mammalian cells that were infected with a helper nonreplicating fowlpox virus.
The plasmids used to implement the repressilat...

The plasmids used to implement the repressilator in Escherichia coli. (Photo credit: Wikipedia)

There are two types of plasmid integration int...

There are two types of plasmid integration into a host bacteria: Non-integrating plasmids replicate as with the top instance, whereas episomes, the lower example, integrate into the host chromosome. (Photo credit: Wikipedia)

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Rewriting the Mathematics of Tumor Growth[1]; Teams Use Math Models to Sort Drivers from Passengers[2]:  Two JNCI Reviews by Mike Martin Regarding Genomics, Cancer, and Mutation

Curator: Stephen J. Williams, Ph.D.

Recently, there has been extensive interest in the cancer research and oncology community on detecting those mutations responsible for the initiation and propagation of a neoplastic cell (driver mutations) versus those mutations that are randomly (or by selective pressures) acquired due to the genetic instability of the transformed cell.  The impact of either type of mutation has been a topic for debate, with a recent article showing that some passenger mutations may actually be responsible for tumor survival.  In addition many articles, highlighted on this site (and referenced below) in recent years have described the importance of classifying driver and passenger mutations for the purposes of more effective personalized medicine strategies directed against tumors. Two review articles by Mike Martin in the Journal of the National Cancer Institute (JCNI) shed light on the current efforts and successes to discriminate between these passenger and driver mutations and determine impact of each type of mutation to tumor growth.  However, as described in the associated article, the picture is not as clear cut as previously thought and highlights some revolutionary findings. In Rewriting the Mathematics of Tumor Growth, researchers discovered that driver mutations may confer such a small growth advantage that, multiple mutations, including the so called passenger mutations are necessary in order to sustain tumor growth. In fact, much experimental evidence has suggested at least six defined genetic events may be necessary for the in-vitro transformation of human cells.  The following table shows some of the genetic events required for in-vitro transformation in cell culture systems.

Genetic events required for transformation

 Species  Cell type  # of genes required for tumor formation*  Genes used  Reference Events required for priming
Human FibroblastsEmbryonic kidney 3 hTERTH-rasLarge T (a)Hahn(Weinberg) 2LT+hTERT
Mammary epithelialMyoblastsEmbryonic kidney 6 hTERTH-rasP53DDc-myc

cyclin D1CDK4

(b)Kendall(Counter) Hras required for tumorigenesis so probably 5 events needed
Fibroblasts 4 Large TSmall TH-rashTERT (c)Sun(Hornsby) 2Large T + H-ras
Fibroblasts 4 Large TSmall ThTERTRas (d)Rangarajan(Weinberg) 3hTERT, Ras and either small or largeT
Keratinocytes 4 CyclinD1

dnp53

EGFR

c-myc

(e)Goessel(Opitz) 3 for anchorage independence (cyclin D1, dnp53, EGFR),Cyclin D1+dnp53 for immortalization
HOSE 6 CDK4, cyclin D, hTERT plus combination of either P53DD, myrAkt, and H-ras or P53DD, H-ras, c-myc Bcl2 (f)Sasaki(Kiyono) 5
HOSE 3 hTERTSV40 earlyH-ras orK-ras (g)Liu(Bast) 2hTERT+ SV40 early
HOSE 3 Large ThTERTH-ras orc-erB-2 (h)Kusakari(Fujii) 2hTERT+large T
Rat Fibroblasts 2 Large TH-ras (i)Hirakawa Did not analyze
Fibroblasts 2 Large TH-ras (d)Rangarajan(Weinberg) Large T
Mouse MOSEIn p53-/- background 3 c-mycK-rasAkt (j)Orsulic
Pig Fibroblasts 6 p53DDhTERT

CDK4H-ras c-myc

cyclin D1

(k)Adam(Counter) 5 need all butp53DD

Note: priming means events required to immortalize but not fully transform.  * Note that both ability to form colonies in soft agarose and subsequently tested for tumor formation in immunocompromised mice.

a.         Hahn, W. C., Counter, C. M., Lundberg, A. S., Beijersbergen, R. L., Brooks, M. W., and Weinberg, R. A. (1999) Creation of human tumour cells with defined genetic elements, Nature 400, 464-468.

b.         Kendall, S. D., Linardic, C. M., Adam, S. J., and Counter, C. M. (2005) A network of genetic events sufficient to convert normal human cells to a tumorigenic state, Cancer Res 65, 9824-9828.

c.         Sun, B., Chen, M., Hawks, C. L., Pereira-Smith, O. M., and Hornsby, P. J. (2005) The minimal set of genetic alterations required for conversion of primary human fibroblasts to cancer cells in the subrenal capsule assay, Neoplasia 7, 585-593.

d.         Rangarajan, A., Hong, S. J., Gifford, A., and Weinberg, R. A. (2004) Species- and cell type-specific requirements for cellular transformation, Cancer Cell 6, 171-183.

e.         Goessel, G., Quante, M., Hahn, W. C., Harada, H., Heeg, S., Suliman, Y., Doebele, M., von Werder, A., Fulda, C., Nakagawa, H., Rustgi, A. K., Blum, H. E., and Opitz, O. G. (2005) Creating oral squamous cancer cells: a cellular model of oral-esophageal carcinogenesis, Proc Natl Acad Sci U S A 102, 15599-15604.

f.          Sasaki, R., Narisawa-Saito, M., Yugawa, T., Fujita, M., Tashiro, H., Katabuchi, H., and Kiyono, T. (2009) Oncogenic transformation of human ovarian surface epithelial cells with defined cellular oncogenes, Carcinogenesis 30, 423-431.

g.         Liu, J., Yang, G., Thompson-Lanza, J. A., Glassman, A., Hayes, K., Patterson, A., Marquez, R. T., Auersperg, N., Yu, Y., Hahn, W. C., Mills, G. B., and Bast, R. C., Jr. (2004) A genetically defined model for human ovarian cancer, Cancer Res 64, 1655-1663.

h.         Kusakari, T., Kariya, M., Mandai, M., Tsuruta, Y., Hamid, A. A., Fukuhara, K., Nanbu, K., Takakura, K., and Fujii, S. (2003) C-erbB-2 or mutant Ha-ras induced malignant transformation of immortalized human ovarian surface epithelial cells in vitro, Br J Cancer 89, 2293-2298.

i.          Hirakawa, T., and Ruley, H. E. (1988) Rescue of cells from ras oncogene-induced growth arrest by a second, complementing, oncogene, Proc Natl Acad Sci U S A 85, 1519-1523.

j.          Orsulic, S., Li, Y., Soslow, R. A., Vitale-Cross, L. A., Gutkind, J. S., and Varmus, H. E. (2002) Induction of ovarian cancer by defined multiple genetic changes in a mouse model system, Cancer Cell 1, 53-62.

k.         Adam, S. J., Rund, L. A., Kuzmuk, K. N., Zachary, J. F., Schook, L. B., and Counter, C. M. (2007) Genetic induction of tumorigenesis in swine, Oncogene 26, 1038-1045.

However it may be argued that the aforementioned experimental examples were produced in cell lines with a more stable genome than that which is seen in most tumors and had used traditional assays of transformation, such as growth in soft agarose and tumorigenicity in immunocompromised mice, as endpoints of transformation, and not representative of the tumor growth seen in the clinical setting.

Therefore Bert Vogelstein, M.D., along with collaborators around the world developed a model they termed the “sequential driver mutation theory”, in which they describe that driver mutations multiply over time with each mutation “slightly increasing the tumor growth rate through a process that depends on three factors”:

  1. Driver mutation rate
  2. The 0.4% selective growth advantage
  3. Cell division time

This model was based on a combination of experimental data and computer simulations of gliobastoma multiforme and pancreatic adenocarcinoma.  Most tumor models follow a Gompertz kinetics, which show how tumor growth is exponential but eventually levels off over time.

This new theory shows though that a tumor cell with only one driver mutation can only grow so much, until a second driver mutation is required.  Using data for the COSMIC database (Catalog of Somatic Mutations in Cancer) together with analysis software CHASM (Cancer-specific High-throughput Annotation of Somatic Mutations) the researchers analyzed 713 mutations sequenced from 14 glioma patients and 562 mutations in nine pancreatic adenocarcinomas, revealing at least 100 tumor suppressor genes and 100 oncogenes altered.  Therefore, the authors suggested these may be possible driver mutations, or at least mutations required for the sustained growth of these tumors.  Applying this new model to data obtained from Dr. Giardiello’s publication concerning familial adenopolypsis in New England Journal of medicine in 19993 and 2000, the sequential driver mutation model predicted age distribution of FAP patients, number and size of polyps, and polyp growth rate than previous models.  This surprising number of required driver mutations for full transformation was also verified in a study led by University of Texas Southwestern Medical Center biologist Jerry Shay, Ph.D., who noted “this team’s surprise nearly 45% of all colorectal candidate oncogenes (65 mutations) drove malignant proliferation”[3].

However, some investigators do not believe the model is complex enough to account for other factors involved in oncogenesis, such as epigenetic factors like methylation and acetylation.  In addition the review also discusses host and tissue factors which may complicate the models, such as location where a tumor develops.  However, most of the investigators interviewed for this review agreed that focusing on this long-term progression of the disease may give us clues to other potential druggable targets.

Teams Use Math Models to Sort Drivers From Passengers

A related review from Mike Martin in JNCI [2] describes a statistical method, published in 2009 Cancer Informatics[4], which distinguishes chromosomal abnormalities that can drive oncogenesis from passenger abnormalities.  Chromosomal abnormalities, such as deletions, additions, and translocations are common in cancer.  For instance, the well-known Philadelphia chromosome, a translocation between chromosome 9 and 22 which results in the BCR-ABL tyrosine kinase fusion protein is the molecular basis of chronic myelogenous leukemia.

In the report, Eytan Domany, Ph.D., from Weizmann Institute and several colleagues from University of Lausanne, University of Haifa and the Broad Institute were analyzing chromosomal aberrations in a subset of medulloblastoma, which had more gain and losses in chromosomes than had been attributed to the disease.  Using a statistical method they termed a “volumetric sieve”, the investigators were able to identify driver versus passenger aberrations based on three filters:

  • Fraction of patients with the abnormality
  • Length of DNA involved in the aberrant chromosome
  • Abnormality’s copy number

Another method to sort the most “important” chromosomal aberrations from less relevant alterations is termed GISTIC[5], as the website describes is: a tool to identify genes targeted by somatic copy-number alterations (SCNAs) that drive cancer growth (at the Broad Institute website http://www.broadinstitute.org/software/cprg/?q=node/31).  The method allows for comparison across multiple tumors so noise is eliminated and improves consistency of analysis.  This method had been successfully used to determine driver aberrations is mesotheliomas, leukemias, and identify new oncogenes in adenocarcinomas of the lung and squamous cell carcinoma of the esophagus.

Main references for the two Mike Martin articles are as follows:

1.         Martin M: Rewriting the mathematics of tumor growth. Journal of the National Cancer Institute 2011, 103(21):1564-1565.

2.         Martin M: Aberrant chromosomes: teams use math models to sort drivers from passengers. Journal of the National Cancer Institute 2010, 102(6):369-371.

3.         Eskiocak U, Kim SB, Ly P, Roig AI, Biglione S, Komurov K, Cornelius C, Wright WE, White MA, Shay JW: Functional parsing of driver mutations in the colorectal cancer genome reveals numerous suppressors of anchorage-independent growth. Cancer research 2011, 71(13):4359-4365.

4.         Shay T, Lambiv WL, Reiner-Benaim A, Hegi ME, Domany E: Combining chromosomal arm status and significantly aberrant genomic locations reveals new cancer subtypes. Cancer informatics 2009, 7:91-104.

5.         Beroukhim R, Getz G, Nghiemphu L, Barretina J, Hsueh T, Linhart D, Vivanco I, Lee JC, Huang JH, Alexander S et al: Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proceedings of the National Academy of Sciences of the United States of America 2007, 104(50):20007-20012.

Further posts on CANCER and GENOMICS and Sequencing published on the site include:

The Initiation and Growth of Molecular Biology and Genomics

Inaugural Genomics in Medicine – The Conference Program, 2/11-12/2013, San Francisco, CA

LEADERS in Genome Sequencing of Genetic Mutations for Therapeutic Drug Selection in Cancer Personalized Treatment: Part 2

Paradigm Shift in Human Genomics – Predictive Biomarkers and Personalized Medicine – Part 1

Breast Cancer: Genomic profiling to predict Survival: Combination of Histopathology and Gene Expression Analysis

Computational Genomics Center: New Unification of Computational Technologies at Stanford

GSK for Personalized Medicine using Cancer Drugs needs Alacris systems biology model to determine the in silico effect of the inhibitor in its “virtual clinical trial”

arrayMap: Genomic Feature Mining of Cancer Entities of Copy Number Abnormalities (CNAs) Data

Comprehensive Genomic Characterization of Squamous Cell Lung Cancers

Mosaicism’ is Associated with Aging and Chronic Diseases like Cancer: detection of genetic mosaicism could be an early marker for detecting cancer.

http://onlinelibrary.wiley.com/doi/10.1111/j.1755-148X.2011.00905.x/full

https://pharmaceuticalintelligence.com/2013/02/05/winning-over-cancer-progression-new-oncology-drugs-to-suppress-driver-mutations-vs-passengers-mutations/

Additional references:

[1] Michor F, Iwasa Y, and Nowak MA (2004) Dynamics of cancer

progression. Nature Reviews Cancer 4, 197-205.

[2] Crespi B and Summers K (2005) Evolutionary biology of cancer.

Trends in Ecology and Evolution 20, 545-552.

[3] Merlo LMF, et al. (2006) Cancer as an evolutionary and ecological

process. Nature Reviews Cancer 6, 924-935.

[4] McFarland C, et al. “Accumulation of deleterious passenger mutations

in cancer,” in preparation.

[5] Birkbak NJ, et al. (2011) Paradoxical relationship between

chromosomal instability and survival outcome in cancer. Cancer

Research 71,3447-3452.

Read Full Post »


Curator: Aviva Lev-Ari, PhD, RN

Chaperon Protein Mechanism inspired MIT Team to Model the Role of Genetic Mutations on Cancer Progression, proposing the next generation of Oncology drugs to aim at Suppression of Passenger Mutations. Current drug, in clinical trials, use the Chaperon Protein Mechanism to suppress Driver Mutations.

Deleterious Mutations in Cancer Progression

Kirill S. Korolev1, Christopher McFarland2, and Leonid A. Mirny3

1Department of Physics, MIT, Cambridge, MA.

E-mail: papers.korolev@gmail.com

2Graduate Program in Biophysics, Harvard University, Cambridge, MA.

3Health Sciences and Technology, MIT, Cambridge, MA

The research was funded by the National Institutes of Health/National Cancer Institute Physical Sciences Oncology Center at MIT.

SOURCE:

http://cnls.lanl.gov/q-bio/wiki/images/4/40/Abstract.pdf

Deleterious passenger mutations significantly affect evolutionary dynamics of cancer. Including passenger mutations in evolutionary models is necessary to understand the role of genetic diversity in cancer progression and to create new treatments based on the accumulation of deleterious passenger mutations.

Evolutionary models of cancer almost exclusively focus on the acquisition of driver mutations, which are beneficial to cancer cells. The driver mutations, however, are only a small fraction of the mutations found in tumors. The other mutations, called passenger mutations, are typically neglected because their effect on fitness is assumed to be very small. Recently, it has been suggested that some passenger mutations are slightly deleterious. We find that deleterious passengers significantly affect cancer progression. In particular, they lead to a critical tumor size, below which tumors shrink on average, and to an optimal mutation rate for cancer evolution.

ANCER is an outcome of somatic evolution [1-3]. To outcompete their benign sisters, cancer cells need to acquire many heritable changes (driver mutations) that enable proliferation. In addition to the rare beneficial drivers, cancer cells must also acquire neutral or slightly deleterious passenger mutations [4]. Indeed, the number of possible passengers exceeds the number of possible drivers by orders of magnitude. Surprisingly, the effect of passenger mutations on cancer progression has not been explored. To address this problem, we developed an evolutionary model of cancer progression, which includes both drivers and passengers. This model was analyzed both numerically and analytically to understand how mutation rate, population size, and fitness effects of mutations affect cancer progression.

RESULTS

Upon including passengers in our model, we found that cancer is no longer a straightforward progression to malignancy. In particular, there is a critical population size such that smaller populations accumulate passengers and decline, while larger populations accumulate drivers and grow. The transition to cancer for small initial populations is, therefore, stochastic in nature and is similar to diffusion over an energy barrier in chemical kinetics. We also found that there is an optimal mutation rate for cancer development, and passengers with intermediate fitness costs are most detrimental to cancer. The existence of an optimal mutation rate could explain recent clinical data [5] and is in stark contrast to the predictions of the models neglecting passengers. We also show that our theory is consistent with recent sequencing data.

SOURCE:

http://cnls.lanl.gov/q-bio/wiki/images/4/40/Abstract.pdf

Just as some mutations in the genome of cancer cells actively spur tumor growth, it would appear there are also some that do the reverse, and act to slow it down or even stop it, according to a new US study led by MIT.

Senior author, Leonid Mirny, an associate professor of physics and health sciences and technology at MIT, and colleagues, write about this surprise finding in a paper to be published online this week in the Proceedings of the National Academy of Sciences.

In a statement released on Monday, Mirny tells the press:

“Cancer may not be a sequence of inevitable accumulation of driver events, but may be actually a delicate balance between drivers and passengers.”

“Spontaneous remissions or remissions triggered by drugs may actually be mediated by the load of deleterious passenger mutations,” he suggests.

Cancer Cell‘s Genome Has “Drivers” and “Passengers”

Your average cancer cell has a genome littered with thousands of mutations and hundreds of mutated genes. But only a handful of these mutated genes are drivers that are responsible for the uncontrolled growth that leads to tumors.

Up until this study, cancer researchers have mostly not paid much attention to the “passenger” mutations, believing that because they were not “drivers”, they had little effect on cancer progression. 

Now Mirny and colleagues have discovered, to their surprise, that the “passengers” aren’t there just for the ride. In sufficient numbers, they can slow down, and even stop, the cancer cells from growing and replicating as tumors. 

New Drugs Could Target the Passenger Mutations in Protein Chaperoning

Although there are already several drugs in development that target the effect of chaperone proteins in cancer, they are aiming to suppress driver mutations.

Recently, biochemists at the University of Massachusetts Amherst“trapped” a chaperone in action, providing a dynamic snapshot of its mechanism as a way to help development of new drugs that target drivers.

But Mirny and colleagues say there is now another option: developing drugs that target the same chaperoning process, but their aim would be to encourage the suppressive effect of the passenger mutations.

They are now comparing cells with identical driver mutations but different passenger mutations, to see which have the strongest effect on growth.

They are also inserting the cells into mice to see which are the most likely to lead to secondary tumors (metastasize).

Written by Catharine Paddock PhD
Copyright: Medical News Today

SOURCE:

http://www.medicalnewstoday.com/articles/255920.php

After proteins are synthesized, they need to be folded into the correct shape, and chaperones help with that process. In cancerous cells, chaperones help proteins fold into the correct shape even when they are mutated, helping to suppress the effects of deleterious mutations.
Several potential drugs that inhibit chaperone proteins are now in clinical trials to treat cancer, although researchers had believed that they acted by suppressing the effects of driver mutations, not by enhancing the effects of passengers.

In current studies, the researchers are comparing cancer cell lines that have identical driver mutations but a different load of passenger mutations, to see which grow faster. They are also injecting the cancer cell lines into mice to see which are likeliest to metastasize.

Drugs that tip the balance in favor of the passenger mutations could offer a new way to treat cancer, the researchers say, beating it with its own weapon — mutations. Although the influence of a single passenger mutation is minuscule, “collectively they can have a profound effect,” Mirny says. “If a drug can make them a little bit more deleterious, it’s still a tiny effect for each passenger, but collectively this can build up.”

In natural populations, selection weeds out deleterious mutations. However, Mirny and his colleagues suspected that the evolutionary process in cancer can proceed differently, allowing mutations with only a slightly harmful effect to accumulate.

If enough deleterious passengers are present, their cumulative effects can slow tumor growth, the simulations found. Tumors may become dormant, or even regress, but growth can start up again if new driver mutations are acquired. This matches the cancer growth patterns often seen in human patients.

“Spontaneous remissions or remissions triggered by drugs may actually be mediated by the load of deleterious passenger mutations.”

When they analyzed passenger mutations found in genomic data taken from cancer patients, the researchers found the same pattern predicted by their model — accumulation of large quantities of slightly deleterious mutations.

REFERENCE

Massachusetts Institute of Technology (2013, February 4). Some cancer mutations slow tumor growth. ScienceDaily. Retrieved February 4, 2013, from http://www.sciencedaily.com­/releases/2013/02/130204154011.htm

Biochemists Trap A Chaperone Machine In Action

Main Category: Biology / Biochemistry
Article Date: 11 Dec 2012 – 0:00 PST

Molecular chaperones have emerged as exciting new potential drug targets, because scientists want to learn how to stop cancer cells, for example, from using chaperones to enable their uncontrolled growth. Now a team of biochemists at the University of Massachusetts Amherst led by Lila Gierasch have deciphered key steps in the mechanism of the Hsp70 molecular machine by “trapping” this chaperone in action, providing a dynamic snapshot of its mechanism.

She and colleagues describe this work in the current issue of Cell. Gierasch’s research on Hsp70 chaperones is supported by a long-running grant to her lab from NIH’s National Institute for General Medical Sciences.

Molecular chaperones like the Hsp70s facilitate the origami-like folding of proteins, made in the cell’s nanofactories or ribosomes, from where they emerge unstructured like noodles. Proteins only function when folded into their proper structures, but the process is so difficult under cellular conditions that molecular chaperone helpers are needed. 

The newly discovered information about chaperone action is important because all rapidly dividing cells use a lot of Hsp70, Gierasch points out. “The saying is that cancer cells are addicted to Hsp70 because they rely on this chaperone for explosive new cell growth. Cancer shifts our body’s production of Hsp70 into high gear. If we can figure out a way to take that away from cancer cells, maybe we can stop the out-of-control tumor growth. To find a molecular way to inhibit Hsp70, you’ve got to know how it works and what it needs to function, so you can identify its vulnerabilities.”

Chaperone proteins in cells, from bacteria to humans, act like midwives or bodyguards, protecting newborn proteins from misfolding and existing proteins against loss of structure caused by stress such as heat or a fever. In fact, the heat shock protein (Hsp) group includes a variety of chaperones active in both these situations.

As Gierasch explains, “New proteins emerge into a challenging environment. It’s very crowded in the cell and it would be easy for them to get their sticky amino acid chains tangled and clumped together. Chaperones bind to them and help to avoid this aggregation, which is implicated in many pathologies such as neurodegenerative diseases. This role of chaperones has also heightened interest in using them therapeutically.”

However, chaperones must not bind too tightly or a protein can’t move on to do its job. To avoid this, chaperones rapidly cycle between tight and loose binding states, determined by whether ATP or ADP is bound. In the loose state, a protein client is free to fold or to be picked up by another chaperone that will help it fold to do its cellular work. In effect, Gierasch says, Hsp70s create a “holding pattern” to keep the protein substrate viable and ready for use, but also protected.

She and colleagues knew the Hsp70’s structure in both tight and loose binding affinity states, but not what happened between, which is essential to understanding the mechanism of chaperone action. Using the analogy of a high jump, they had a snapshot of the takeoff and landing, but not the top of the jump. “Knowing the end points doesn’t tell us how it works. There is a shape change in there that we wanted to see,” Gierasch says.

To address this, she and her colleagues postdoctoral fellows Anastasia Zhuravleva and Eugenia Clerico obtained “fingerprints” of the structure of Hsp70 in different states by using state-of-the-art nuclear magnetic resonance (NMR) methods that allowed them to map how chemical environments of individual amino acids of the protein change in different sample conditions. Working with an Hsp70 known as DnaK from E. coli bacteria, Zhuravleva and Clerico assigned its NMR spectra. In other words, they determined which peaks came from which amino acids in this large molecule.

The UMass Amherst team then mutated the Hsp70 so that cycling between tight and loose binding states stopped. As Gierasch explains, “Anastasia and Eugenia were able to stop the cycle part-way through the high jump, so to speak, and obtain the molecular fingerprint of a transient intermediate.” She calls this accomplishment “brilliant.”

Now that the researchers have a picture of this critical allosteric state, that is, one in which events at one site control events in another, Gierasch says many insights emerge. For example, it appears nature uses this energetically tense state to “tune” alternate versions of Hsp70 to perform different cellular functions. “Tuning means there may be evolutionary changes that let the chaperone work with its partners optimally,” she notes.

“And if you want to make a drug that controls the amount of Hsp70 available to a cell, our work points the way toward figuring out how to tickle the molecule so you can control its shape and its ability to bind to its client. We’re not done, but we made a big leap,” Gierasch adds. “We now have a idea of what the Hsp70 structure is when it is doing its job, which is extraordinarily important.” 

Article adapted by Medical News Today from original press release. Click ‘references’ tab above for source.
Visit our biology / biochemistry section for the latest news on this subject.
SOURCE:

REFERENCES

[1] Michor F, Iwasa Y, and Nowak MA (2004) Dynamics of cancer

progression. Nature Reviews Cancer 4, 197-205.

[2] Crespi B and Summers K (2005) Evolutionary biology of cancer.

Trends in Ecology and Evolution 20, 545-552.

[3] Merlo LMF, et al. (2006) Cancer as an evolutionary and ecological

process. Nature Reviews Cancer 6, 924-935.

[4] McFarland C, et al. “Accumulation of deleterious passenger mutations

in cancer,” in preparation.

[5] Birkbak NJ, et al. (2011) Paradoxical relationship between

chromosomal instability and survival outcome in cancer. Cancer

Research 71,3447-3452.

Other related articles on this Open Access Online Scientific Journal include the following:

Hold on. Mutations in Cancer do good.

https://pharmaceuticalintelligence.com/2013/02/04/hold-on-mutations-in-cancer-do-good/

Rational Design of Allosteric Inhibitors and Activators Using the Population-Shift Model: In Vitro Validation and Application to an Artificial Biosensor

https://pharmaceuticalintelligence.com/2012/10/26/rational-design-of-allosteric-inhibitors-and-activators-using-the-population-shift-model-in-vitro-validation-and-application-to-an-artificial-biosensor/

LEADERS in Genome Sequencing of Genetic Mutations for Therapeutic Drug Selection in Cancer Personalized Treatment: Part 2

https://pharmaceuticalintelligence.com/2013/01/13/leaders-in-genome-sequencing-of-genetic-mutations-for-therapeutic-drug-selection-in-cancer-personalized-treatment-part-2/

Exome sequencing of serous endometrial tumors shows recurrent somatic mutations in chromatin-remodeling and ubiquitin ligase complex genes

https://pharmaceuticalintelligence.com/2012/12/18/exome-sequencing-of-serous-endometrial-tumors-shows-recurrent-somatic-mutations-in-chromatin-remodeling-and-ubiquitin-ligase-complex-genes/

Genome-Wide Detection of Single-Nucleotide and Copy-Number Variation of a Single Human Cell(1)

https://pharmaceuticalintelligence.com/2013/02/03/genome-wide-detection-of-single-nucleotide-and-copy-number-variation-of-a-single-human-cell/

Gastric Cancer: Whole-genome reconstruction and mutational signatures

https://pharmaceuticalintelligence.com/2012/12/24/gastric-cancer-whole-genome-reconstruction-and-mutational-signatures-2/

Pregnancy with a Leptin-Receptor Mutation

https://pharmaceuticalintelligence.com/2012/10/31/pregnancy-with-a-leptin-receptor-mutation/

Mitochondrial mutation analysis might be “1-step” away

https://pharmaceuticalintelligence.com/2012/08/14/mitochondrial-mutation-analysis-might-be-1-step-away/

Genome-wide Single-Cell Analysis of Recombination Activity and De Novo Mutation Rates in Human Sperm

https://pharmaceuticalintelligence.com/2012/08/07/genome-wide-single-cell-analysis-of-recombination-activity-and-de-novo-mutation-rates-in-human-sperm/

A Prion Like-Protein, Protein Kinase Mzeta and Memory Maintenance

https://pharmaceuticalintelligence.com/2012/10/19/a-prion-like-protein-protein-kinase-mzeta-and-memory-maintenance/

Hope for Male Contraception: A small molecule that inhibits a protein important for chromatin organization can cause reversible sterility in male mice

https://pharmaceuticalintelligence.com/2012/09/03/hope-for-male-contraception-a-small-molecule-that-inhibits-a-protein-important-for-chromatin-organization-can-cause-reversible-sterility-in-male-mice/

Protein Folding may lead to better FLU Vaccine

https://pharmaceuticalintelligence.com/2012/07/25/protein-folding-may-lead-to-better-flu-vaccine/

SNAP: Predict Effect of Non-synonymous Polymorphisms: How well Genome Interpretation Tools could Translate to the Clinic

https://pharmaceuticalintelligence.com/2013/02/03/snap-predict-effect-of-non-synonymous-polymorphisms-how-well-genome-interpretation-tools-could-translate-to-the-clinic/

Drugging the Epigenome

https://pharmaceuticalintelligence.com/2013/02/01/drugging-the-epigenome/

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Reporter: Prabodh Kandala, PhD

A typical cancer cell has thousands of mutations scattered throughout its genome and hundreds of mutated genes. However, only a handful of those genes, known as drivers, are responsible for cancerous traits such as uncontrolled growth. Cancer biologists have largely ignored the other mutations, believing they had little or no impact on cancer progression.

But a new study from MIT, Harvard University, the Broad Institute and Brigham and Women’s Hospital reveals, for the first time, that these so-called passenger mutations are not just along for the ride. When enough of them accumulate, they can slow or even halt tumor growth.

The findings, reported in this week’sProceedings of the National Academy of Sciences, suggest that cancer should be viewed as an evolutionary process whose course is determined by a delicate balance between driver-propelled growth and the gradual buildup of passenger mutations that are damaging to cancer, says Leonid Mirny, an associate professor of physics and health sciences and technology at MIT and senior author of the paper.

Furthermore, drugs that tip the balance in favor of the passenger mutations could offer a new way to treat cancer, the researchers say, beating it with its own weapon — mutations. Although the influence of a single passenger mutation is minuscule, “collectively they can have a profound effect,” Mirny says. “If a drug can make them a little bit more deleterious, it’s still a tiny effect for each passenger, but collectively this can build up.”

Lead author of the paper is Christopher McFarland, a graduate student at Harvard. Other authors are Kirill Korolev, a Pappalardo postdoctoral fellow at MIT, Gregory Kryukov, a senior computational biologist at the Broad Institute, and Shamil Sunyaev, an associate professor at Brigham and Women’s.

Power struggle

Cancer can take years or even decades to develop, as cells gradually accumulate the necessary driver mutations. Those mutations usually stimulate oncogenes such as Ras, which promotes cell growth, or turn off tumor-suppressing genes such as p53, which normally restrains growth.

Passenger mutations that arise randomly alongside drivers were believed to be fairly benign: In natural populations, selection weeds out deleterious mutations. However, Mirny and his colleagues suspected that the evolutionary process in cancer can proceed differently, allowing mutations with only a slightly harmful effect to accumulate.

To test this theory, the researchers created a computer model that simulates cancer growth as an evolutionary process during which a cell acquires random mutations. These simulations followed millions of cells: every cell division, mutation and cell death.

They found that during the long periods between acquisition of driver mutations, many passenger mutations arose. When one of the cancerous cells gains a new driver mutation, that cell and its progeny take over the entire population, bringing along all of the original cell’s baggage of passenger mutations. “Those mutations otherwise would never spread in the population,” Mirny says. “They essentially hitchhike on the driver.”

This process repeats five to 10 times during cancer development; each time, a new wave of damaging passengers is accumulated. If enough deleterious passengers are present, their cumulative effects can slow tumor growth, the simulations found. Tumors may become dormant, or even regress, but growth can start up again if new driver mutations are acquired. This matches the cancer growth patterns often seen in human patients.

“Cancer may not be a sequence of inevitable accumulation of driver events, but may be actually a delicate balance between drivers and passengers,” Mirny says. “Spontaneous remissions or remissions triggered by drugs may actually be mediated by the load of deleterious passenger mutations.”

When they analyzed passenger mutations found in genomic data taken from cancer patients, the researchers found the same pattern predicted by their model — accumulation of large quantities of slightly deleterious mutations.

Tipping the balance

In computer simulations, the researchers tested the possibility of treating tumors by boosting the impact of deleterious mutations. In their original simulation, each deleterious passenger mutation reduced the cell’s fitness by about 0.1 percent. When that was increased to 0.3 percent, tumors shrank under the load of their own mutations.

The same effect could be achieved in real tumors with drugs that interfere with proteins known as chaperones, Mirny suggests. After proteins are synthesized, they need to be folded into the correct shape, and chaperones help with that process. In cancerous cells, chaperones help proteins fold into the correct shape even when they are mutated, helping to suppress the effects of deleterious mutations.

Several potential drugs that inhibit chaperone proteins are now in clinical trials to treat cancer, although researchers had believed that they acted by suppressing the effects of driver mutations, not by enhancing the effects of passengers.

In current studies, the researchers are comparing cancer cell lines that have identical driver mutations but a different load of passenger mutations, to see which grow faster. They are also injecting the cancer cell lines into mice to see which are likeliest to metastasize.

Ref:

Massachusetts Institute of Technology (2013, February 4). Some cancer mutations slow tumor growth. ScienceDaily. Retrieved February 4, 2013, from http://www.sciencedaily.com­/releases/2013/02/130204154011.htm

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Reporter: Aviva Lev-Ari, RN

With New Microfludic Technique, MIT Team Aims to ‘Squeeze’ siRNAs into Cells

January 31, 2013

Researchers from the Massachusetts Institute of Technology last week reported on the development of a new microfluidic-based approach to delivering macromolecules, including functional siRNAs, into cells without the need for a vector.

According to the investigators, who published their findings in the Proceedings of the National Academy of Sciences, the technique involves compressing cells by passing them through a constriction, which opens up temporary holes in their membranes that permit the diffusion of materials in surrounding buffer to enter the cytosol.

“By providing flexibility in application and obviating the need for exogenous materials or electrical fields, this method could potentially enable new avenues of disease research and treatment,” they wrote.

Although intracellular delivery of macromolecules is a key step in therapeutic and research applications, the cellular membrane is largely impermeable to such compounds, according to the PNAS paper. Existing methods to overcome this hurdle, which has proven to be a major stumbling block for RNAi drugs, typically involve the use of polymeric nanoparticles, liposomes, or chemical modifications of the target molecules to facilitate membrane poration or endocytotic delivery.

When it comes to nucleic acids, which are relatively structurally uniform, these approaches can be efficient. Still, the “endosome escape mechanism that most of these methods rely on is often inefficient; hence, much material remains trapped in endosomal and lysosomal vesicles,” the MIT team pointed out. “More effective gene delivery methods, such as viral vectors, however, often risk chromosomal integration.

Meantime, electroporation has proven effective, even in difficult to transfect primary cells, but has limited applicability and can cause cell death. Microinjection, too, has certain advantages in settings such as the creation of transgenic organisms, but its low throughput hamstrings many therapeutic and research applications, the researchers noted.

To overcome the limitations of existing delivery techniques, the MIT group had initially been attempting to “shoot” molecules of interest into cells, Armon Sharei, an MIT graduate student in chemical engineering and lead author of the PNAS paper, told Gene Silencing News.

“That system had its own challenges, and through the course of that work, we stumbled upon this effect where if you squeeze the cells rapidly enough, it will temporarily disrupt their membrane,” he said.

More specifically, the researchers found that the “rapid mechanical deformation of a cell, as it passes through a constriction with a minimum dimension smaller than the cell diameter, results in the formation of transient membrane disruptions or holes,” they wrote in PNAS. “The size and frequency of these holes would be a function of the shear and compressive forces experienced by the cell during its passage through the constriction. Material from the surrounding medium may then diffuse directly into the cell cytosol throughout the life span of these holes.”

To test this idea, the researchers constructed devices, each consisting of 45 identical, parallel microfluidic channels containing one or more constrictions, etched onto a silicon chip and sealed in glass. The width of each constriction ranged from 4 to 8 micrometers, and the lengths ranged from 10 to 40 micrometers.

“Before use, the device is first connected to a steel interface that connects the inlet and outlet reservoirs to the silicon device,” the researchers wrote. “A mixture of cells and the desired delivery material is then placed into the inlet reservoir and Teflon tubing is attached at the inlet. A pressure regulator is then used to adjust the pressure at the inlet reservoir and drive the cells through the device. Treated cells are collected from the outlet reservoir.”

The system was tested with a variety of molecules, including carbon nanotubes and proteins, as well as siRNAs targeting GFP. According to Sharei, when the siRNAs were delivered into GFP-expressing HeLa cells using the microfluidic platform, the investigators were able to achieve 80 to 90 percent target knockdown.

He noted that the knockdown effects weren’t as robust as with Lipofectamine 2000, but “we were still encouraged because something like Lipofectamine is known to be toxic and therefore inapplicable for humans.” Notably, the microfluidic device and operating parameters were not optimized for siRNAs, further limiting its ability to compete with the transfection reagent in these studies.

“The other good thing was that we seem to work just as well for primary cells, whereas existing methods like Lipofectamine don’t translate well once you start moving out of the standard cell models you have in the lab,” he added.

The MIT team also successfully delivered 3 kilodalton dextran molecules — which are approximately the same size as a standard siRNA molecule and a “pretty accurate” surrogate for the gene-silencing molecules — into newborn human foreskin fibroblasts, primary murine dendritic cells, and embryonic stem cells, suggesting that the method could be used with siRNAs into a variety of cell types, Sharei said.

Buoyed by the positive data, he and his colleagues are now further testing the platform with siRNAs against “easy readout genes” in primary cells including immune cells and stem cells, he said. “Once we establish that, we’d try to go for an application where there’s an siRNA that’s going to knock down something functional.

“I can’t say exactly what we’ve been up to because it’s not published, but it has been going pretty well,” he added.

Ultimately, the MIT group aims to develop the microfluidic platform not only for research applications, where it could be “incorporated into a larger integrated system consisting of multiple pre-treatment and post-treatment modules” that could take advantage of its average throughput rate of 20,000 cells a second, but also therapeutic ones, too.

A number of investigational stem cell-based therapies, for instance, involve the ex vivo manipulation of the cells, Sharei said. The delivery platform could theoretically be used to “enhance or facilitate that manipulation.”

“Such an approach would take advantage of the potentially increased delivery efficiency of therapeutic macro- molecules and could be safer than existing techniques because it would obviate the need for potentially toxic vector particles and would mitigate any potential side effects associated with reticuloendothelial clearance and off-target delivery,” the study authors wrote in PNAS.

Doug Macron is the editor of GenomeWeb’s Gene Silencing News. He covers research and therapeutic applications of RNAi, miRNA, and other gene-silencing technologies. E-mail Doug Macron or follow his GenomeWeb Twitter account at@Genesilencing.

 

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State of the art in oncologic imaging of breast.

Author-Writer: Dror Nir, PhD

In the coming posts I will address the state of the art in oncologic imaging based on a review paper; Advances in oncologic imaging that provides updates on the latest approaches to imaging of 5 common cancers: breast, lung, prostate, colorectal cancers, and lymphoma. This paper is published at CA Cancer J Clin 2012. © 2012 American Cancer Society.

The paper gives a fair description of the use of imaging in interventional oncology based on literature review of more than 200 peer-reviewed publications.

In this post I summaries the chapter on breast cancer imaging.

Breast Cancer Imaging

As a start the authors describes the evolution in the ACS imaging guidelines for breast cancer screening. Most interesting to learn is how age limits are changing. The most recent: “In 2010, the Society of Breast Imaging and the Breast Imaging Commission of the ACS issued recommendations for breast cancer screening to provide guidance in light of the controversies and emerging technologies.5 These recommendations were based on multiple prospective randomized trials as well as population-based experience.

Recommendations for screening with non-mammographic imaging are based not on evidence showing mortality reduction but largely on surrogate indicators, i.e., tumor size and nodal status, suggesting improved survival compared with women who are not screened.” I have referred to these guidelines in my recent post: Not applying evidence-based medicine drives up the costs of screening for breast-cancer in the USA.

As long as imaging interpretation is based mainly on observations related to lesion morphology:

“The imaging characteristics of malignant lesions are nonspecific and usually do not allow a definitive diagnosis. When a biopsy is recommended based on mammography, it has a 25% to 45% likelihood of resulting in a diagnosis of carcinoma.11 Similar positive predictive values are reported for biopsies recommended based on MRI.”

It is worthwhile noting that these results do not reflect purely the specificity of the imaging device but rather the specificity of the whole workflow; i.e imaging, biopsy and histopathology. All imaging techniques have false negatives: Mammography screening of general population misses approximately 20% of the cancers. This rate increases as breast density increases. MRI is not applied to general population. When applied to highly suspicious cases MRI misses ~10% of the invasive cancers. Although ultrasound has proven to be useful in detecting cancer especially in women with dense breasts: Automated Breast Ultrasound System (‘ABUS’) for full breast scanning: The beginning of structuring a solution for an acute need! Based on the literature reviewed by the authors of this paper they do not recommend routine sonography for these women.

For women with locally advanced breast cancer (Fig. 2) who undergo neoadjuvant therapy before breast surgery, the authors recommends post-treatment staging using MRI, which has been found to predict complete response with sensitivity above 60% and specificity as high as 90%.26

A 27-year-old female with locally advanced poorly differentiated invasive ductal carcinoma underwent evaluation of extent of disease before starting neoadjuvant chemotherapy. Sagittal fat-suppressed T1-weighted postcontrast MR images demonstrate an almost 6-cm heterogeneously enhancing mass (A) involving the skin of the lower breast (arrow) with (B) right axillary (arrow) and (C) right internal mammary adenopathy (arrow).

A 27-year-old female with locally advanced poorly differentiated invasive ductal carcinoma underwent evaluation of extent of disease before starting neoadjuvant chemotherapy. Sagittal fat-suppressed T1-weighted postcontrast MR images demonstrate an almost 6-cm heterogeneously enhancing mass (A) involving the skin of the lower breast (arrow) with (B) right axillary (arrow) and (C) right internal mammary adenopathy (arrow).

Same is recommended for women who have undergone lumpectomy if the surgical margins are positive. As post therapy follow-up, a new baseline mammogram of the treated breast is recommended followed by annual mammography.

In regards to emerging technology the following are discussed: Mammographic tomosynthesis – see also Improving Mammography-based imaging for better treatment planning

Contrast-enhanced digital mammography – “involves the injection of iodinated contrast material, as is done for computed tomography (CT); this enables hypervascular lesions to be seen with modified mammography technology, potentially providing the same information obtained through MRI. Little has been published on the clinical application of this technology, but diagnostic accuracy better than that of mammography and approaching that of MRI has been reported.3132

MR choline spectroscopy – has been shown to improve the positive predictive value of breast MRI and may be useful in reducing the number of lesions that require biopsy (Fig. 4).33 Studies of spectroscopy have reported sensitivities of 70% to 100% and specificities of 67% to 100% in the detection of breast cancer. Decreasing choline concentrations may also be a useful indication of tumor response to treatment before any change in tumor volume can be detected.3435 Technical factors have limited the use of spectroscopy to lesions 1 cm in size or larger.”

Sagittal fat-suppressed T1-weighted postcontrast MR image is shown (A) of the right breast of a 48-year-old female who was status post–contralateral mastectomy for DCIS with the spectroscopy voxel placed over an enhancing mass (arrow). The magnified spectrum (B) demonstrated no choline peak. Biopsy yielded fibroadenoma.

Sagittal fat-suppressed T1-weighted postcontrast MR image is shown (A) of the right breast of a 48-year-old female who was status post–contralateral mastectomy for DCIS with the spectroscopy voxel placed over an enhancing mass (arrow). The magnified spectrum (B) demonstrated no choline peak. Biopsy yielded fibroadenoma.

Diffusion-weighted MRI (DW-MRI) – “adding DW-MRI data to other imaging characteristics of lesions on breast MRI may increase the positive predictive value of the examination, in turn decreasing the number of benign lesions requiring biopsy for diagnosis.” See also Imaging: seeing or imagining? (Part 2).

Axial T1-weighted fat-suppressed postcontrast MR image is shown (A) of the left breast of a 42-year-old female with biopsy-proven contralateral cancer undergoing evaluation of disease extent. An enhancing mass (arrow) was seen in the left breast. This mass (arrow) was also demonstrated on the axial diffusion-weighted MR image (B). Biopsy yielded fibroadenoma with atypical ductal hyperplasia and lobular carcinoma in situ.

Axial T1-weighted fat-suppressed postcontrast MR image is shown (A) of the left breast of a 42-year-old female with biopsy-proven contralateral cancer undergoing evaluation of disease extent. An enhancing mass (arrow) was seen in the left breast. This mass (arrow) was also demonstrated on the axial diffusion-weighted MR image (B). Biopsy yielded fibroadenoma with atypical ductal hyperplasia and lobular carcinoma in situ.

Ultrasound-elastography – “Ultrasound elastography has been reported to differentiate benign from malignant breast lesions with sensitivities of 78% to 100% and specificities of 21% to 98%.39 When added to other US techniques, it may improve radiologists’ performance in distinguishing malignant breast lesions.”

Positron emission tomography (PET) – “alone or combined with CT, allows noninvasive, quantitative assessment of biochemical and functional processes at the molecular level in the body. It is most often performed with the radiolabeled glucose analogue [18F] fluorodeoxyglucose ([18F]FDG) to detect the elevated glucose metabolism that is a hallmark of cancer. In breast cancer, its utility depends on the pretest probability for advanced disease, and thus the clinical stage.” The authors found that the use of [18F] FDG PET to patients with stage I and II disease is “limited”. Specifically, they claim that it is not sufficiently accurate for axillary nodal staging in this subset of patients.40 The did find enough evidence to recommend the use of FDG PET in patients with advanced disease: “where it accurately defines disease extent,41 and frequently eliminates the need for other imaging tests, and provides an early readout of treatment response as well as prognostic information.”

Combined PET/MRI is mentioned as a promising technology for predicting response to therapy “but this remains to be proven”.

Positron emission mammography (PEM) – “adapts full-body PET imaging to the breast. In a multicenter study, the interpretation of PEM in conjunction with mammographic and clinical findings yielded a sensitivity of 91% and a specificity of 93% for breast cancer.47 “. However, the authors mention that its use for screening (applying to healthy women) has been criticized because of the need to administer a radioactive tracer.

Lung Cancer Imaging

To be followed…

Other research papers related to the management of breast cancer were published on this Scientific Web site:

The unfortunate ending of the Tower of Babel construction project and its effect on modern imaging-based cancer patients’ management

 Automated Breast Ultrasound System (‘ABUS’) for full breast scanning: The beginning of structuring a solution for an acute need!

Introducing smart-imaging into radiologists’ daily practice.

Will Bio-Tech make Medical Imaging redundant?

Improving Mammography-based imaging for better treatment planning

Not applying evidence-based medicine drives up the costs of screening for breast-cancer in the USA.

New Imaging device bears a promise for better quality control of breast-cancer lumpectomies – considering the cost impact

Harnessing Personalized Medicine for Cancer Management, Prospects of Prevention and Cure: Opinions of Cancer Scientific Leaders @ http://pharmaceuticalintelligence.com

Predicting Tumor Response, Progression, and Time to Recurrence

“The Molecular pathology of Breast Cancer Progression”

Personalized medicine gearing up to tackle cancer

Whole-body imaging as cancer screening tool; answering an unmet clinical need?

What could transform an underdog into a winner?

Mechanism involved in Breast Cancer Cell Growth: Function in Early Detection & Treatment

Nanotech Therapy for Breast Cancer

A Strategy to Handle the Most Aggressive Breast Cancer: Triple-negative Tumors

Optical Coherent Tomography – emerging technology in cancer patient management

Breakthrough Technique Images Breast Tumors in 3-D With Great Clarity, Reduced Radiation

Closing the Mammography gap

Imaging: seeing or imagining? (Part 1)

Imaging: seeing or imagining? (Part 2)

 

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Author: Aviva Lev-Ari, PhD,RN

UPDATED on 5/8/2013

Cardiosonic Begins Enrollment in the TIVUS I Renal Denervation Trial

April 24, 2013

April 24, 2013 — Cardiosonic Inc. announced the completion of the first phase of patient enrollment in its first-in-man (FIM) TIVUS I clinical study. The study is designed to collect data on the safety and performance of the TIVUS System, a high intensity, non-focused therapeutic ultrasound catheter system for remote tissue ablation for the treatment of hypertension by renal denervation (RDN).

The study enrolled the first five patients at Royal Perth Hospital (RPH), Australia and patient screening is continuing. Sharad Shetty, M.D., principal investigator at RPH, completed the procedures with a 100 percent acute success rate in accessing the vessels and delivering therapy. “The performance of renal denervation with an advanced, ultrasonic catheter has been shown to be quick, easy and seems to be associated with minimal pain. The TIVUS System by Cardiosonic has great potential to become an important technology for management of resistant hypertensive patients,” commented Shetty. Shetty will present interim results from the FIM trial at the Euro PCR conference, Paris, May 21 to 24.

The company completed extensive bench and animal studies and following these initial human results is submitting its next human clinical trial to 20 sites worldwide. Krishna Rocha-Singh, an advisor to the company and a leader in the rapidly growing field of RDN, from the Prairie Heart Institute at the St. John’s Hospital in Springfield, Ill., commented that, “The TIVUS system has great potential to improve the process and outcomes of RDN procedures. In addition the TIVUS system may expand the population of patients eligible for RDN therapy by obviating current anatomic and physiologic restrictions and contra-indications.”

Benny Dilmoney, Cardiosonic CEO, commented that, “We are enthusiastic about completing the first phase of enrollment and progressing towards completion of our FIM patients recruitment and follow-up. Cardiosonic has completed the development of our second generation multi-directional catheter and initiated submission for its study at 20 centers worldwide. We believe that this advanced catheter design will further improve RDN procedures.”

Posted on : 27 November 2012 in 

Renal Sympathetic Denervation: a Rapidly Evolving Field

Written by Dr. Sebastian Mafeld – Radiology Specialist Registrar, Freeman Hospital, Newcastle upon Tyne, UK and Dr. Gerard S Goh – Consultant Interventional Radiologist, St. George’s Healthcare NHS Trust, London, UK.

The 11/27/2012 paper HAS IGNORED THE ALREADY PUBLISHED LITERATURE IN THE FIELD – nothing of the mentioned in it is NEW or innovative — in 2012 that is intolerable !!

The Scientific Honesty is at Stack

PNAS Study: 2/3 of Retractions in Scientific Journals represents Fraud, Duplicate publication, and Plagiarism (Misconduct).

Reporter: Aviva Lev-Ari, PhD, RN

‘We Have a Problem in Science’

October 02, 2012

A recent study in the Proceedings of the National Academy of Sciences found that more than two-thirds of 2,000 retractions in the life science literature were attributable to some form of misconduct, including fraud, duplicate publication, and plagiarism.

The study, led by Arturo Casadevall of Albert Einstein College of Medicine, estimates that the percentage of scientific papers retracted because of fraud has increased more than 10-fold since 1975.

Carl Zimmer notes in The New York Times that previous studies have concluded that most retractions were attributable to “honest errors,” but the new study “challenges that comforting assumption.”

The authors compiled more than 2,000 retraction notices published before May 3, 2012, and then dug into the reasons behind each retraction. Some reasons were cited by the journals, but the authors also found that the retraction notices for some papers did not cite fraud as the reason for the retraction.

The rise in fraudulent papers “is a sign of a winner-take-all culture in which getting a paper published in a major journal can be the difference between heading a lab and facing unemployment,” Zimmer says.

According to Casadevall, the fact that “some fraction of people are starting to cheat” should not be taken lightly, even if the overall number of fraudulent papers is relatively low. “It convinces me more that we have a problem in science,” he says.

 Source:

For the ORIGINAL work on 

Renal Sympathetic Denervation: Updates on the State of Medicine

the Readers is called to go to the ORIGINAL SOURCES listed below:

Intravascular Stimulation of Autonomics: A Letter from Dr. Michael Scherlag

https://pharmaceuticalintelligence.com/2012/09/02/intravascular-stimulation-of-autonomics-a-letter-from-dr-michael-scherlag/

Imbalance of Autonomic Tone: The Promise of Intravascular Stimulation of Autonomics

https://pharmaceuticalintelligence.com/2012/09/02/imbalance-of-autonomic-tone-the-promise-of-intravascular-stimulation-of-autonomics/

Interaction of Nitric Oxide and Prostacyclin in Vascular Endothelium

https://pharmaceuticalintelligence.com/2012/09/14/interaction-of-nitric-oxide-and-prostacyclin-in-vascular-endothelium/

Absorb™ Bioresorbable Vascular Scaffold: An International Launch by Abbott Laboratories

https://pharmaceuticalintelligence.com/2012/09/29/absorb-bioresorbable-vascular-scaffold-an-international-launch-by-abbott-laboratories/

The Molecular Biology of Renal Disorders: Nitric Oxide – Part III

https://pharmaceuticalintelligence.com/2012/11/26/the-molecular-biology-of-renal-disorders/

Treatment of Refractory Hypertension via Percutaneous Renal Denervation

https://pharmaceuticalintelligence.com/2012/06/13/treatment-of-refractory-hypertension-via-percutaneous-renal-denervation/

Renal Denervation Technology of Vessix Vascular, Inc. been acquired by Boston Scientific Corporation (BSX) to pay up to $425 Million

https://pharmaceuticalintelligence.com/2012/11/08/renal-denervation-technology-of-vessix-vascular-inc-been-acquired-by-boston-scientific-corporation-bsx-to-pay-up-to-425-million/

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Larry H. Bernstein, MD, Reporter

This is another very interesting contribution.  I submit without change.

Neuroscientists find the molecular “when”, “where” of memory formation
Fri, 10/19/2012 – 11:30am

Neuroscientists from New York University and the University of California, Irvine have isolated the “when” and “where” of molecular activity that occurs in the formation of short-, intermediate-, and long-term memories. Their findings, which appear the Proceedings of the National Academy of Sciences, offer new insights into the molecular architecture of memory formation and, with it, a better roadmap for developing therapeutic interventions for related afflictions.

“Our findings provide a deeper understanding of how memories are created,” explains the research team leader Thomas Carew, a professor in NYU’s Center for Neural Science and dean of NYU’s Faculty of Arts and Science. “Memory formation is not simply a matter of turning molecules on and off; rather, it results from a complex temporal and spatial relationship of molecular interaction and movement.”

Neuroscientists have previously uncovered different aspects of molecular signaling relevant to the formation of memories. But less understood is the spatial relationship between molecules and when they are active during this process.

To address this question, the researchers studied the neurons inAplysia californica, the California sea slug. Aplysia is a model organism that is quite powerful for this type of research because its neurons are 10 to 50 times larger than those of higher organisms, such as vertebrates, and it possesses a relatively small network of neurons—characteristics that readily allow for the examination of molecular signaling during memory formation. Moreover, its coding mechanism for memories is highly conserved in evolution, and thus is similar to that of mammals, making it an appropriate model for understanding how this process works in humans.

The scientists focused their study on two molecules, MAPK and PKA, which earlier research has shown to be involved in many forms of memory and synaptic plasticity—that is, changes in the brain that occur after neuronal interaction. But less understood was how and where these molecules interacted.

English: Figure 1: A possible mechanism of cAM...

English: Figure 1: A possible mechanism of cAMP/PKA inhibition of ERK activation (MAPK pathway). cAMP activation of PKA activates Rap1 via Src. Rap1 then phosphorylates Ras and inhibits signaling to Raf-1. (Photo credit: Wikipedia)

To explore this, the researchers subjected the sea slugs to sensitization training, which induces increased behavioral reflex responsiveness following mild tail shock, or in this study, mild activation of the nerve form the tail. They then examined the subsequent molecular activity of both MAPK and PKA. Both molecules have been shown to be involved in the formation of memory for sensitization, but the nature of their interaction is less clear.

What they found was MAPK and PKA coordinate their activity both spatially and temporally in the formation of memories. Specifically, in the formation of intermediate-term (for example, hours) and long-term (for example, days) memories, both MAPK and PKA activity occur, with MAPK spurring PKA action. By contrast, for short-term memories (for example, less than 30 min), only PKA is active, with no involvement of MAPK.

Source: New York University

 

 

 

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Author: Tilda Barliya PhD

Title: Building a DSS: choice of polymers and drugs

Category: Nanotechnology and drug delivery

During the last 40 years, controlled drug delivery has become one of the most challenging and rapidly advancing scientific areas. Delivery systems can offer numerous advantages compared to conventional dosage forms. This coalition of polymeric science and pharmaceutical science led to the innovation in the design and development of drug delivery systems (DDS). Some of the challenges of most drug delivery systems include poor bioavailability, in vivo stability, solubility, intestinal absorption, sustained and targeted delivery to site of action, therapeutic effectiveness, side effects and patient compliance as well as plasma fluctuations of drugs which either fall below the minimum effective concentrations or exceed the safe therapeutic concentrations.

The purpose of these polymers in such system is to increase the delivery effectiveness of drugs to pathological cells by protecting them from degradation in the physiological environment, localize the drug to the desired site and be non-toxic.  (1,3,4 ).

Grund S and colleagues nicely outlined the history of polymer-based drug delivery system, the types of polymers and drug combinations (1).

Classification:

–          Origin (synthetic, natural or both)

–          Chemical nature (polyester, polyanhydride etc)

–          Backbone stability (biodegradable or not)

–          Water solubility (hydrophilic, hydrophobic) and Electrical charges

Although intertwined, delivery systems can be generally grouped as:

–          Biodegradable drug delivery systems

–          Diffusion controlled drug delivery system

–          Responsive drug delivery system (thermo, pH, enzymatic)

These DDS systems among others are differentiated on the basis of the mechanism controlling the release of the drug from the polymers (1,2).

Biodegradable polymers disintegrate into biocompatible compounds when exposed to chemicals (like water), enzymes or microbial which leaves the incorporated drug behind.  The drug molecule present in the DDS is released due to the process of erosion. Moreover, the degradation of the polymers involves breakdown of polymers and reduction by the Kreb’s cycle to carbon dioxide and water.  Furthermore, biodegradable polymers can be manipulated by the addition of functional/liable groups such as: esters, amine, urea, anhydride, carbonates etc to the backbone.  Here are some examples to the most common biodegradable polymers; polyesters, polyacrylic acids,  polyanhydride, polyurea etc

Diffusion controlled-polymer systems involve the dispersion of the therapeutic molecule within the polymer shell. The sustained release of the drug from this system is driven by diffusion through the pores or between the polymer chains. Drug: Progestasert (intra-uterine), Nicoderm (transdermal)

Responsive drug delivery systems release the drug in a more controlled manner which can be stimulated by the surrounding such as temperature, solvent, pH and/or concentration. Poly (N-isopropylacrylamide) is a well known example for a thermo-responsive polymer. Poly (ethylene glycol), poly lactic acid etc are known to be used for their thermogelling system.  Drug: Atridox.

 A different way to approach drug delivery system is:

–          Temporal controlled

–          Distribution controlled

In temporal control DDS, the aim is to deliver the drug a specific time during the treatment and controlled release over extended duration is highly beneficial for drugs that are rapidly metabolized and eliminated from the body after administration (2)

in distribution controlled DDS, the aim is to the deliver the drug to a specific site in the body.  This delivery system is highly beneficial when natural distribution encounter body cells and cause major side effects that prohibit further treatment ( i.e chemotherapy) or when natural distribution can’t be facilitated using the regular systemic system (i.e passing the BBB and reaching brain tumors)

The choice of drugs imposed various restrictions on the type of the delivery system employed.

For example, a drug that is to be released over an extended period in a patient’s stomach where the pH is acidic and environmental conditions fluctuate widely will require a controlled release system very different from that of a drug that is to be delivered in a pulsatile manner within the blood system.

It is also very important to understand the fate of the polymer after the drug has been released, such as polymers that naturally excreted from the body (kidneys), removed after the drug release (patch or and insert) or extract through the GI track, are acceptable in medical application.

Four physicochemical properties of polymers can affect the opsonisation process and determine the degree of RES clearance (1):

  • Charge
  • Molecular size
  • Shape
  • Hydrophobicity/lipophilicity

In summary

Polymer science has become the motor for the development of new drug delivery systems in the past decades and requires an increasingly intensive cooperation between chemists, technologists and biologists.

“Over the years, especially induced by the introduction of micro- and nanosized carriers, they have changed their profile to parenteral drug applications and are now capable of offering advanced, more sophisticated and multifunctional approaches such as stealth effects and drug targeting for medicines. Combination therapy applying multiple types of drugs concurrently with one single drug delivery system will lead to more effective therapeutics and a more convenient application for the patients”

Novel, tailored polymers with more complicated and complex structures and functions may influence many related scientific and regulatory fields. However, several questions regarding regulatory approval of polymer-based carriers are still pending, and the establishment of new guidelines and policies especially adapted to nanosized polymer materials and their unique properties is still in the beginning. New criteria to determine identity, purity, and stability of the materials during manufacturing and storage have to be
defined and confirmed by new validated analytical methods.

References

  1. Grund S, Bauer M and Fischer D.   Polymers in drug delivery-State of the art and future trends. Advanced Engineering Materials 2011, 13(3); B61-B87. http://onlinelibrary.wiley.com/doi/10.1002/adem.201080088/abstract
  2. Unrich K.E, Cannizzaro S.N and Langer R.S.  Polymeric systems for controlled Drug release. Chem. Rev. 1999, 99; 3181−3198. http://www.qmc.ufsc.br/qmcweb/artigos/dor/bonus/Polymeric%20Systems%20for%20Controlled%20Drug%20Release.pdf
  3. Mody V.V. Introduction ro polymeric drug delivery. Internet journal of medical update 2010; 5(2): 1-2 http://www.akspublication.com/Editorial_Jul2010_.pdf
  4. Muhammad T, Nur Z, Piletska E.V, Yimit O and Piletsky S.A.Rational design of molecularly imprinted polymer: the choice of cross-linker.  Analyst.  2012 Jun 7;137(11):2623-8. Epub 2012 Apr 26. http://pubs.rsc.org/en/content/articlelanding/2012/AN/C2AN35228
  5. Torchilin VA. Polymeric Immunomicelles: Carriers of Choice for Targeted Delivery of Water-Insoluble Pharmaceuticals. Drug Delivery Tech 2004: 4(2). http://www.drugdeliverytech.com/ME2/dirmod.asp?sid=&nm=&type=Publishing&mod=Publications%3A%3AArticle&mid=8F3A7027421841978F18BE895F87F791&tier=4&id=5F2B931260F14B7786C80C84E46AEC1
  6. William B. Liechty W.B, David R. Kryscio D.R, Brandon V. Slaughter B.V and Peppas N.A. Polymers for Drug Delivery Systems. Annual Review of Chemical and Biomolecular Engineering 2010 1: 149-173. http://www.annualreviews.org/doi/abs/10.1146/annurev-chembioeng-073009-100847.
  7. Chen Y and Liu L. Modern methods for delivery of drugs across the blood–brain barrierAdv Drug Deliv Rev 2012: 64(7); 640-665. http://www.sciencedirect.com/science/article/pii/S0169409X11002900.
  8. Kaparissides C, Alexandridou S, Kotti K and Chaitidou S. Recent Advances in Novel Drug Delivery Systems. Journal on nanotechnology online. March 2006. http://www.azonano.com/article.aspx?ArticleID=1538

Key words: polymers, drug delivery system, materials, nanotechnology

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Reporter: Aviva Lev-Ari, PhD, RN

 

‘We Have a Problem in Science’

October 02, 2012

A recent study in the Proceedings of the National Academy of Sciences found that more than two-thirds of 2,000 retractions in the life science literature were attributable to some form of misconduct, including fraud, duplicate publication, and plagiarism.

The study, led by Arturo Casadevall of Albert Einstein College of Medicine, estimates that the percentage of scientific papers retracted because of fraud has increased more than 10-fold since 1975.

Carl Zimmer notes in The New York Times that previous studies have concluded that most retractions were attributable to “honest errors,” but the new study “challenges that comforting assumption.”

The authors compiled more than 2,000 retraction notices published before May 3, 2012, and then dug into the reasons behind each retraction. Some reasons were cited by the journals, but the authors also found that the retraction notices for some papers did not cite fraud as the reason for the retraction.

The rise in fraudulent papers “is a sign of a winner-take-all culture in which getting a paper published in a major journal can be the difference between heading a lab and facing unemployment,” Zimmer says.

According to Casadevall, the fact that “some fraction of people are starting to cheat” should not be taken lightly, even if the overall number of fraudulent papers is relatively low. “It convinces me more that we have a problem in science,” he says.

 Source:

 http://www.genomeweb.com//node/1133746?hq_e=el&hq_m=1361468&hq_l=1&hq_v=09187c3305

Misconduct accounts for the majority of retracted scientific publications

  1. Ferric C. Fanga,b,1,
  2. R. Grant Steenc,1, and
  3. Arturo Casadevalld,1,2

+Author Affiliations


  1. Departments of aLaboratory Medicine and

  2. bMicrobiology, University of Washington School of Medicine, Seattle, WA 98195;

  3. cMediCC! Medical Communications Consultants, Chapel Hill, NC 27517; and

  4. dDepartment of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461
  1. Edited by Thomas Shenk, Princeton University, Princeton, NJ, and approved September 6, 2012 (received for review July 18, 2012)

Abstract

A detailed review of all 2,047 biomedical and life-science research articles indexed by PubMed as retracted on May 3, 2012 revealed that only 21.3% of retractions were attributable to error. In contrast, 67.4% of retractions were attributable to misconduct, including fraud or suspected fraud (43.4%), duplicate publication (14.2%), and plagiarism (9.8%). Incomplete, uninformative or misleading retraction announcements have led to a previous underestimation of the role of fraud in the ongoing retraction epidemic. The percentage of scientific articles retracted because of fraud has increased ∼10-fold since 1975. Retractions exhibit distinctive temporal and geographic patterns that may reveal underlying causes.

Footnotes

  • Author contributions: F.C.F., R.G.S., and A.C. designed research, performed research, analyzed data, and wrote the paper.

  • The authors declare no conflict of interest.

  • This article is a PNAS Direct Submission.

  • This article contains supporting information online atwww.pnas.org/lookup/suppl/doi:10.1073/pnas.1212247109/-/DCSupplemental.

    Source:

    http://www.pnas.org/content/early/2012/09/27/1212247109.abstract

     

    Misconduct Widespread in Retracted Science Papers, Study Finds

    By CARL ZIMMER
    Published: October 1, 2012

    Last year the journal Nature reported an alarming increase in the number of retractions of scientific papers — a tenfold rise in the previous decade, to more than 300 a year across the scientific literature.

    Other studies have suggested that most of these retractions resulted from honest errors. But a deeper analysis of retractions, being published this week, challenges that comforting assumption.

    In the new study, published in the Proceedings of the National Academy of Sciences, two scientists and a medical communications consultant analyzed 2,047 retracted papers in the biomedical and life sciences. They found that misconduct was the reason for three-quarters of the retractions for which they could determine the cause.

    “We found that the problem was a lot worse than we thought,” said an author of the study, Dr. Arturo Casadevall of Albert Einstein College of Medicine in the Bronx.

    Dr. Casadevall and another author, Dr. Ferric C. Fang of the University of Washington, have been outspoken critics of the current culture of science. To them, the rising rate of retractions reflects perverse incentives that drive scientists to make sloppy mistakes or even knowingly publish false data.

    “We realized we would really like more hard data for what the reasons were for retractions,” Dr. Fang said.

    They began collaborating with R. Grant Steen, a medical communications consultant in Chapel Hill, N.C., who had already published a study on 10 years of retractions. Together they gathered all the retraction notices published before May 2012 by searching PubMed, a database of scientific literature maintained by the National Library of Medicine.

    “I guess our O.C.D. kicked in and we started trying to look at every paper we could look at,” Dr. Fang said.

    The researchers analyzed the reasons for retractions cited by the scientific journals. But they also looked beyond the journals for the full story.

    In the mid-2000s, for example, Boris Cheskis, then a senior scientist at Wyeth Research, and his colleagues published two papers on estrogen. Later, the scientists retracted both papers, explaining that some of the data in them were “unreliable.” In 2010, the Office of Research Integrity at the federal Department of Health and Human Services ruled that Dr. Cheskis had engaged in misconduct, having falsified the figures.

    Dr. Cheskis settled with the government. Although he neither accepted nor denied the charges, he agreed not to serve on any advisory boards for the United States Public Health Service and agreed to be supervised on any Public Health Service-financed research for two years.

    Neither of the notices for the two retracted papers has been updated to reflect the finding of fraud. Dr. Cheskis could not be reached for comment.

    Dr. Fang and his colleagues dug through other reports from the Office of Research Integrity, as well as newspaper articles and the blog Retraction Watch. All told, they reclassified 158 papers as fraudulent based on their extra research.

    “We haven’t seen this level of analysis before,” said Dr. Ivan Oransky, an author of Retraction Watch and the executive editor at Reuters Health. “It confirms what we suspected.”

    Dr. Oransky said he expected the rise to continue in the near future. He and his co-author, Adam Marcus, have been scrambling to keep up with new cases of fraud.

    In July, for example, the Japanese Society of Anesthesiologists reported that Dr. Yoshitaka Fujii had falsified data in 172 papers. Most of those papers have yet to be officially retracted. “They’re headed for the fraud pile,” Dr. Oransky said.

    Dr. Benjamin G. Druss, a professor of health policy of Emory University, said he found the statistics in the paper to be sound but added that they “need to be kept in perspective.” Only about one in 10,000 papers in PubMed have been officially retracted, he noted. By contrast, 112,908 papers have had published corrections.

    Dr. Casadevall disagreed. “It convinces me more that we have a problem in science,” he said.

    While the fraudulent papers may be relatively few, he went on, their rapid increase is a sign of a winner-take-all culture in which getting a paper published in a major journal can be the difference between heading a lab and facing unemployment. “Some fraction of people are starting to cheat,” he said.

    Better policing techniques, like plagiarism-detecting software, might help slow the rise in misconduct, Dr. Casadevall said, but the most important thing the scientific community can do is change its culture.

    “I don’t think this problem is going to go away as long as you have this disproportionate system of rewards,” he said.

    <nyt_correction_bottom>

    This article has been revised to reflect the following correction:

    Correction: October 1, 2012

     

    An earlier version of this story misstated the federal agency housing the Office of Research Integrity. It is the Department of Health and Human Services, not the National Institutes of Health. The earlier version also misstated the reason cited in the study for three-quarters of the retractions for which researchers could determine the cause. It was misconduct, not fraud. (Fraud or suspected fraud accounted for 41.3 percent of retractions; other forms of misconduct made up the rest.)

    Source:

    http://www.nytimes.com/2012/10/02/science/study-finds-fraud-is-widespread-in-retracted-scientific-papers.html?_r=1 

 

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