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Posts Tagged ‘screening’

LIVE 9/21 8AM to 10:55 AM Expoloring the Versatility of CRISPR/Cas9 at CHI’s 14th Discovery On Target, 9/19 – 9/22/2016, Westin Boston Waterfront, Boston

http://www.discoveryontarget.com/

http://www.discoveryontarget.com/crispr-therapies/

Leaders in Pharmaceutical Business Intelligence (LPBI) Group is a

Media Partner of CHI for CHI’s 14th Annual Discovery on Targettaking place September 19 – 22, 2016 in Boston.

In Attendance, streaming LIVE using Social Media

Aviva Lev-Ari, PhD, RN

Editor-in-Chief

http://pharmaceuticalintelligence.com

#BostonDOT16

@BostonDOT

 

COMMENTS BY Stephen J Williams, PhD

EXPLORING THE VERSATILITY OF CRISPR/Cas9

 

8:00 Chairperson’s Opening Remarks

TJ Cradick , Ph.D., Head of Genome Editing, CRISPR Therapeutics

 

@CRISPRTX

 

8:10 Functional Genomics Using CRISPR-Cas9: Technology and Applications

Neville Sanjana, Ph.D., Core Faculty Member, New York Genome Center and Assistant Professor, Department of Biology & Center for Genomics and Systems Biology, New York University

 

CRISPR Cas9 is easier to target to multiple genomic loci; RNA specifies DNA targeting; with zinc finger nucleases or TALEEN in the protein specifies DNA targeting

 

  • This feature of crisper allows you to make a quick big and cheap array of a GENOME SCALE Crisper Knock out (GeCKO) screening library
  • How do you scale up the sgRNA for whole genome?; for all genes in RefSeq, identify consitutive exons using RNA-sequencing data from 16 primary human tissue (alot of genes end with ‘gg’) changing the bases on 3’ side negates crisper system but changing on 5’ then crisper works fine
  • Rank sequences to be specific for target
  • Cloned array into lentiviral and put in selectable markers
  • GeCKO displays high consistency betweens reagents for the same gene versus siRNA; GeCKO has high screening sensitivity
  • 98% of genome is noncoding so what about making a library for intronic regions (miRNA, promoter regions?)
  • So you design the sgRNA library by taking 100kb of gene-adjacent regions
  • They looked at CUL3; (data will soon be published in Science)
  • Do a transcription CHIP to verify the lack of binding of transcription factor of interest
  • Can also target histone marks on promoter and enhancer elements
  • NYU wants to explore this noncoding screens
  • sanjanalab.org

 

@nyuniversity

 

8:40 Therapeutic Gene Editing With CRISPR/Cas9

TJ Cradick , Ph.D., Head of Genome Editing, CRISPR Therapeutics

 

NEHJ is down and dirty repair of single nonhomologous end but when have two breaks the NEHJ repair can introduce the inversions or deletions

 

    • High-throughput screens are fine but can limit your view of genomic context; genome searches pick unique sites so use bioinformatic programs  to design specific guide Rna
    • Bioinformatic directed, genome wide, functional screens
    • Compared COSMID and CCTOP; 320 COSMID off-target sites, 333 CCtop off target
    • Young lab GUIDESeq program genome wide assay useful to design guides
    • If shorten guide may improve specificity; also sometime better sensitivity if lengthen guide

 

  • Manufacturing of autologous gene corrected product ex vivo gene correction (Vertex, Bayer, are partners in this)

 

 

They need to use a clones from multiple microarrays before using the GUidESeq but GUIDEseq is better for REMOVING the off targets than actually producing the sgRNA library you want (seems the methods for library development are not fully advanced to do this)

 

The score sometimes for the sgRNA design programs do not always give the best result because some sgRNAs are genome context dependent

9:10 Towards Combinatorial Drug Discovery: Mining Heterogeneous Phenotypes from Large Scale RNAi/Drug Perturbations

Arvind Rao, Ph.D., Assistant Professor, Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center

 

Bioinformatics in CRISPR screens:  they looked at image analysis of light microscopy of breast cancer cells and looked for phenotypic changes

 

  • Then they modeled in a small pilot and then used the algorithm for 20,000 images (made morphometric measurements)
  • Can formulate training statistical algorithms to make a decision tree how you classify data points
  • Although their algorithms worked well there was also human input from scientists

Aggregate ranking of hits programs available on web like LINKS

 

@MDAndersonNews

 

10:25 CRISPR in Stem Cell Models of Eye Disease

Alexander Bassuk, M.D., Ph.D., Associate Professor of Pediatrics, Department of Molecular and Cellular Biology, University of Iowa

 

Blind athlete Michael Stone, biathlete, had eye disease since teenager helped fund and start the clinical trial for Starbardt disease; had one bad copy of ABCA4, heterozygous (inheritable in Ahkenazi Jewish) – a recessive inheritable mutation with juvenile macular degeneration

  • Also had another male in family with disease but he had another mutation in the RPGR gene
  • December 2015 paper Precision Medicine: Genetic Repair of retinitis pigmentosa in patient derived stem cells
  • They were able to correct the iPSCs in the RPGR gene derived from patient however low efficiency of repair, scarless repair, leaves changes in DNA, need clinical grade iPSCs, and need a humanized model of RPGR

@uiowa

10:55 CRISPR in Mouse Models of Eye Disease

Vinit Mahajan, M.D., Ph.D., Assistant Professor of Ophthalmology and Visual Sciences, University of Iowa College of Medicine

  • degeneration of the retina will see brown spots, the macula will often be preserved but retinal cells damaged but with RPGR have problems with peripheral vision, retinitis pigmentosa get tunnel vision with no peripheral vision (a mouse model of PDE6 Knockout recapitulates this phenotype)
  • the PDE6 is linked to the rhodopsin GTP pathway
  • rd1 -/- mouse has something that looks like retinal pigmentosa; has mutant PDE6; is actually a nonsense mutation in rd1 so they tried a crisper to fix in mice
  • with crisper fix of rd1 nonsense mutation the optic nerve looked comparible to normal and the retina structure restored
  • photoreceptors layers- some recovery but not complete
  • sequence results show the DNA is a mosaic so not correcting 100% but only 35% but stil leads to a phenotypic recovery; NHEJ was about 12% to 25% with large deletions
  • histology is restored in crspr repaired mice
  • CRSPR off target effects: WGS and analyze for variants SNV/indels, also looked at on target and off target regions; there were no off target SNVs indels while variants that did not pass quality control screening not a single SNV
  • Rhodopsin mutation accounts for a large % of patients (RhoD190N)
  • injection of gene therapy vectors: AAV vector carrying CRSPR and cas9 repair templates

CAPN mouse models

  • family in Iowa have dominant mutation in CAPN5; retinal degenerates
  • used CRSPR to generate mouse model with mutation in CAPN5 similar to family mutation
  • compared to other transgenic methods CRSPR is faster to produce a mouse model

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Overall good meeting #s:

#personalizedmedicine

#innovation

#cancer

#immunology

#immunooncology

#pharmanews

#CRSPR

#geneediting

#crisper

#biotech

 

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Ultrasound imaging as an instrument for measuring tissue elasticity: “Shear-wave Elastography” VS. “Strain-Imaging”

Writer and curator: Dror Nir, PhD

In the context of cancer-management, imaging is pivotal. For decades, ultrasound is used by clinicians to support every step in cancer pathways. Its popularity within clinicians is steadily increasing despite the perception of it being less accurate and less informative than CT and MRI. This is not only because ultrasound is easily accessible and relatively low cost, but also because advances in ultrasound technology, mainly the conversion into PC-based modalities allows better, more reproducible, imaging and more importantly; clinically-effective image interpretation.

The idea to rely on ultrasound’s physics in order to measure the stiffness of tissue lesions is not new. The motivation for such measurement has to do with the fact that many times malignant lesions are stiffer than non-malignant lesions.

The article I bring below; http://digital.studio-web.be/digitalMagazine?issue_id=254 by Dr. Georg Salomon and his colleagues, is written for lay-readers. I found it on one of the many portals that are bringing quasi-professional and usually industry-sponsored information on health issues; http://www.dieurope.com/ – The European Portal for Diagnostic Imaging. Note, that when it comes to using ultrasound as a diagnostic aid in urology, Dr. Georg Salomon is known to be one of the early adopters for new technologies and an established opinion leader who published many peer-review, frequently quoted, papers on Elastography.

The important take-away I would like to highlight for the reader: Quantified measure of tissue’s elasticity (doesn’t matter if is done by ShearWave or another “Elastography” measure implementation) is information that has real clinical value for the urologists who needs to decide on the right pathway for his patient!

Note: the highlights in the article below are added by me for the benefit of the reader.

Improvement in the visualization of prostate cancer through the use of ShearWave Elastography

by:

Dr Georg Salomon1 Dr Lars Budaeus1, Dr L Durner2 & Dr K Boe1

1. Martini-Clinic — Prostate Cancer Center University Hospital Hamburg Eppendorf Martinistrasse 52, 20253 Hamburg, Germany

2. Urologische Kilnik Dr. Castringius Munchen-Planegg Germeringer Str. 32, 82152 Planegg, Germany

Corresponding author; PD Dr. Georg Salomon

Associate Professor of Urology

Martini Clinic

Tel: 0049 40 7410 51300

gsalornon@uke.de

 

Prostate cancer is the most common cancer in males with more than 910,000 annual cases worldwide. With early detection, excellent cure rates can be achieved. Today, prostate cancer is diagnosed by a randomized transrectal ultrasound guided biopsy. However, such randomized “blind” biopsies can miss cancer because of the inability of conventional TRUS to visualize small cancerous spots in most cases.

Elastography has been shown to improve visualization of prostate cancer.

The innovative ShearWave Elastography technique is an automated, user-friendly and quantifiable method for the determination of prostatic tissue stiffness.

The detection of prostate cancer (PCA) has become easier thanks to Prostate Specific Anti­gen (PSA) testing; the diagnosis of PCA has been shifted towards an earlier stage of the disease.

Prostate cancer is, in more than 80 % of the cases, a heterogeneous and multifocal tumor. Conventional ultra­sound has limitations to accurately define tumor foci within the prostate. This is due to the fact that most PCA foci are isoechogenic, so in these cases there is no dif­ferentiation of benign and malignant tissue. Because of this, a randomized biopsy is performed under ultrasound guidance with at least 10 to 12 biopsy cores, which should represent all areas of the prostate. Tumors, however, can be missed by this biopsy regimen since it is not a lesion-targeted biopsy. When PSA is rising — which usually occurs in most men — the originally negative biopsy has to be repeated.

What urologists expect from imag­ing and biopsy procedures is the detection of prostate cancer at an early stage and an accurate description of all foci within the prostate with different (Gleason) grades of differentiation for best treatment options.

In the past 10 years a couple of new innovative ultrasound techniques (computerized, contrast enhanced and real time elastography) have been introduced to the market and their impact on the detection of early prostate cancer has been evaluated. The major benefit of elastography compared to the other techniques is its ability to provide visualization of sus­picious areas and to guide the biopsy needle, in real time, to the suspicious and potentially malignant area.

Ultrasound-based elastography has been investigated over the years and has had a lot of success for increasing the detection rate of prostate cancer or reducing the number of biopsy sam­ples required. [1-3]. Different compa­nies have used different approaches to the ultrasound elastography technique (strain elastography vs. shear wave elastography). Medical centers have seen an evolution in better image qual­ity with more stable and reproducible results from these techniques.

One drawback of real time strain elastography is that there is a sig­nificant learning curve to be climbed before reproducible elastograms can be generated. The technique has to be performed by compressing and then decompressing the ultrasound probe to derive a measurement of tissue displacement.

Today there are ultrasound scanners on the market, which have the ability to produce elastograms without this “manual” assistance: this technique is called shear-wave elastography. While the ultrasound probe is being inserted transrectally, the “elastograms” are generated automatically by the calcu­lation of shear wave velocity as the waves travel through the tissue being examined, thus providing measure­ments of tissue stiffness and not dis­placement measurements.

There are several different tech­niques for this type of elastography. The FibroScan system, which is not an ultrasound unit, uses shear waves (transient elastography) to evaluate the advancement of the stiffness of the liver. Another technique is Acous­tic Radiation Force Impulse or ARF1 technique, also used for the liver. These non-real-time techniques only provide a shear wave velocity estimation for a single region of interest and are not currently used in prostate imaging.

A shear wave technology that pro­vides specific quantification of tissue elasticity in real-time is ShearWave Elastography, developed by Super-Sonic Imagine. This technique mea­sures elasticity in kilopascals and can provide visual representation of tis­sue stiffness over the entire region of interest in a color-coded map on the ultrasound screen. On a split screen the investigator can see the conven­tional ultrasound B-mode image and the color-coded elastogram at the same time. This enables an anatomi­cal view of the prostate along with the elasticity image of the tissue to guide the biopsy needle.

In short, ShearWave Elastography (SWE) is a different elastography technique that can be used for several applications. It automatically gener­ates a real-time, reproducible, fully quantifiable color-coded image of tissue elasticity.

QUANTIFICATION OF TISSUE STIFFNESS Such quantification can help to increase the chance that a targeted biopsy is positive for cancer.

It has been shown that elastography-targeted biopsies have an up to 4.7 times higher chance to be positive for cancer than a randomized biopsy [4J. Shear-Wave Elastography can not only visual­ize the tissue stiffness in color but also quantify (in kPa) the stiffness in real time, for several organs including the prostate. Correas et al, reported that with tissue stiffness higher than 45 to 50 kPa the chance of prostate cancer is very high in patients undergoing a pros­tate biopsy. The data from Gorreas et al showed a sensitivity of 80 % and a high negative predictive value of up to 9096. Another group (Barr et A) achieved a negative predictive value of up to 99.6% with a sensitivity of 96.2% and specific­ity of 962%. With a cut-off of 4D kPa the positive biopsy rate for the ShearWave Elastography targeted biopsy was 50%, whereas for randomized biopsy it was 20.8 95. In total 53 men were enrolled in this study.

Our group used SWE prior to radical prostatectomy to determine if the Shear-Wave Elastography threshold had a high accuracy using a cutoff >55 kPa. (Fig 1)

We then compared the ShearWave results with the final histopathological results. [Figure I], Our results showed the accuracy was around 78 % for all tumor foci We were also able to verify that ShearWave Elastography targeted biopsies were more likely to be posi­tive compared to randomized biopsies. [Figures 2, 3]

F1

F2F3 

CONCLUSION

SWE is a non-invasive method to visualize prostate cancer foci with high accuracy, in a user-friendly way. As Steven Kaplan puts it in an edi­torial comment in the Journal of Urology 2013: “Obviously, large-scale studies with multicenter corroboration need to be performed. Nevertheless, SWE is a potentially promising modality to increase our efficiency in evaluating prostate diseases:’

 

REFERENCES

  1. Pallweln, L. et al-. Sonoelastography of the prostate: comparison with systematic biopsy findings in 492 patients. European journal of radiology, 2008. 65(2): p. 304-10.
  2. Pallwein, L., et al., Comparison of sono-elastography guided biopsy with systematic biopsy: Impact on prostate cancer detecton. European radiology, 2007_ 17.(9) p. 2278-85.
  3. Salomon, G., et al., Evaluation of prostate can cer detection with ultrasound real-time elas-tographyl a companion with step section path­ological analysis after radical prostatectomy. European urology, 2008. 5446): p. 135462-
  4. Aigner, F., at al., Value of real-time elastography targeted biopsy for prostate cancer detection in men with prostate specific antigen 125 ng/mi or greater and 4-00 ng/ml or Lass. The Journal of urology, 2010. 184{3): p. 813.7,

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

Imaging: seeing or imagining? (Part 1)

Early Detection of Prostate Cancer: American Urological Association (AUA) Guideline

Today’s fundamental challenge in Prostate cancer screening

State of the art in oncologic imaging of Prostate.

From AUA2013: “HistoScanning”- aided template biopsies for patients with previous negative TRUS biopsies 

On the road to improve prostate biopsy

 

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Author and Curator: Dror Nir, PhD

 

As an entrepreneur who is promoting innovations in medical imaging I often find myself confronted with this question. Usually the issue is raised by a project’s potential financier by the way of the following remarks:

  • The Genome Project opens the road to “Star Track” kind of medicine. No one will need imaging.
  • What about development of new disease-specific markers? Would that put imaging out of business?
  • Soon we will have a way to “fix” bad cells’ DNA.  and so we will have no use for screening

In these situations I always find myself struggling to come up with answers rather than simply saying, ‘Well, it will take more time for these applications to be available than for you to reach your exit….’. I always try to find a quantitative citation to show how much time and money still needs to be invested before patients will be able to profit from that kind of futuristic “sci-fi medicine”.

Last week, a very recent source for such information was brought to my attention.  As a contributor to Leaders in Pharmaceutical Business Intelligence I was asked to review and comment on a recent report published in Nature regarding the progress made in the ENCODE project [1]. I was also asked to assess the influence of the progress in understanding the human genome on imaging-based cancer patients’ management, my field of expertise.

This short report is nicely written and is clear to layman’s (which is what I consider myself in this field) reading. My attention was drawn to some important facts:

  • It took 10 years and $288 Million to realise that 80% of 3 Billion DNA bases comprising the human genome serves a purpose.
  • So far a very small percentage (3% to 4%) of this potential was uncovered in the scope of this project.
  • Already now it is clear that much of the “knowledge” regarding the human genome’s functionality will need to be re-written.
  • Researchers anticipate that future studies using advanced technologies will contribute to better estimation of the knowledge gap.
  • Good news: these studies are leading to better understanding of diseases’ pathological characteristics and to more accurate reporting of disease sources. This gives hope to future development of disease specific drug development.

So, back to the subject of this post: it seems to me that we are quite a few decades and many billions of dollars away from “Star-Trek medicine”. In the foreseeable  future, i.e. at least during my life time (and I hope to live a while longer…), the daily routine of cancer patients’ management will have to rely on workflows constituted of screening, diagnosis, a treatment choice that includes a trial and error type of drugs’ choice, and a long-term post treatment follow-up. Smart imaging promises to increase cost efficiency and medical efficacy of these workflows. And I do hope that our children will benefit from the investment our generation is making in understanding the way the human genome is functioning.

  1. Science 7 September 2012: Vol. 337 no. 6099 pp. 1159-1161
    DOI: 10.1126/science.337.6099.1159 http://www.sciencemag.org/content/337/6099/1159.summary?sid=835cf304-a61f-45d5-8d77-ad44b454e448

Written by Dror Nir

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Today’s fundamental challenge in Prostate cancer screening

Author and Curator: Dror Nir, PhD

The management of men with prostate cancer is becoming one of the most challenging public health issues in the Western world. It is characterized by: over-diagnosis; over-treatment; low treatment efficacy; treatment related toxicity; escalating cost; and unsustainability [Bangma et al, 2007; Esserman et al, 2009]. How come? Well, everyone accepts that most prostate cancers are clinically insignificant. It is well known that all men above 65 harbor some sort of prostate cancer. Due to the current aggressive PSA-based screening, one in six men will be diagnosed with prostate cancer. Yet, the lifetime risk of dying of prostate cancer is only 3%. The problem is that, once diagnosed with prostate cancer, there is no accurate tool to identify those men that will die of the disease (in my previous post I mentioned 1:37). Currently, screening practices for prostate cancer are relying on the very unspecific prostate-specific-antigen (PSA) bio-marker test to determine which men are at higher risk of harboring prostate cancer and therefore need a biopsy. The existing diagnostic test is a transrectal ultrasound (TRUS) guided prostate biopsy aimed at extracting representative tissue from areas where cancer usually resides. This procedure suffers from several obvious faults:

1. Since the imaging tool used (B-mode ultrasound) is poor at detecting malignancies in the prostate, the probability of hitting a clinically significant cancer or missing a clinically insignificant cancer is subject to random error.

2. TRUS biopsy is also subjected to systematic error as it misses large parts of the prostate which might harbor cancer (e.g. apex and anterior zones).
3. TRUS guided biopsies are often unrepresentative of the true burden of cancer as either the volume or grade of cancer can be underestimated.

In the last ten years I was leading the development of an innovative ultrasound-based technology, HistoScanningTM, aimed at improving the aforementioned faults;

Among the other most popular imaging modalities aimed at better prostate cancer detection in routine use are: MRIElastography, Contrast Enhanced Ultrasound etc…

In my future posts I will go into more detail on how these imaging modalities fit into routine workflow, how much they stay within budget constraints and what level of promise they bear for promoting personalized medicine. Stay tuned… Footnote: According to the final report by an advisory panel to the USA government: Doctors should no longer offer the PSA prostate cancer screening test to healthy men because they’re more likely to be harmed by the blood draw, and the chain of medical interventions that often follows than be helped; (http://www.usatoday.com/news/health/story/2012-05-21/prostate-cancer-screening-test-harmful/55118036/1) But then; what should be offered instead?

Other posts on this Scientific Website addressing Prostate Cancer

Prostate Cancers Plunged After USPSTF Guidance, Will It Happen Again?

http://pharmaceuticalintelligence.com/2012/07/31/prostate-cancers-plunged-after-uspstf-guidance-will-it-happen-again/

New Prostate Cancer Screening Guidelines Face a Tough Sell, Study Suggests

http://pharmaceuticalintelligence.com/2012/05/27/new-prostate-cancer-screening-guidelines-face-a-tough-sell-study-suggests/

ROLE OF VIRAL INFECTION IN PROSTATE CANCER

http://pharmaceuticalintelligence.com/2012/09/01/role-of-viral-infection-in-prostate-cancer/

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