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Posts Tagged ‘breast cancer’


Showcase: How Deep Learning could help radiologists spend their time more efficiently

Reporter and Curator: Dror Nir, PhD

 

The debate on the function AI could or should realize in modern radiology is buoyant presenting wide spectrum of positive expectations and also fears.

The article: A Deep Learning Model to Triage Screening Mammograms: A Simulation Study that was published this month shows the best, and very much feasible, utility for AI in radiology at the present time. It would be of great benefit for radiologists and patients if such applications will be incorporated (with all safety precautions taken) into routine practice as soon as possible.

In a simulation study, a deep learning model to triage mammograms as cancer free improves workflow efficiency and significantly improves specificity while maintaining a noninferior sensitivity.

Background

Recent deep learning (DL) approaches have shown promise in improving sensitivity but have not addressed limitations in radiologist specificity or efficiency.

Purpose

To develop a DL model to triage a portion of mammograms as cancer free, improving performance and workflow efficiency.

Materials and Methods

In this retrospective study, 223 109 consecutive screening mammograms performed in 66 661 women from January 2009 to December 2016 were collected with cancer outcomes obtained through linkage to a regional tumor registry. This cohort was split by patient into 212 272, 25 999, and 26 540 mammograms from 56 831, 7021, and 7176 patients for training, validation, and testing, respectively. A DL model was developed to triage mammograms as cancer free and evaluated on the test set. A DL-triage workflow was simulated in which radiologists skipped mammograms triaged as cancer free (interpreting them as negative for cancer) and read mammograms not triaged as cancer free by using the original interpreting radiologists’ assessments. Sensitivities, specificities, and percentage of mammograms read were calculated, with and without the DL-triage–simulated workflow. Statistics were computed across 5000 bootstrap samples to assess confidence intervals (CIs). Specificities were compared by using a two-tailed t test (P < .05) and sensitivities were compared by using a one-sided t test with a noninferiority margin of 5% (P < .05).

Results

The test set included 7176 women (mean age, 57.8 years ± 10.9 [standard deviation]). When reading all mammograms, radiologists obtained a sensitivity and specificity of 90.6% (173 of 191; 95% CI: 86.6%, 94.7%) and 93.5% (24 625 of 26 349; 95% CI: 93.3%, 93.9%). In the DL-simulated workflow, the radiologists obtained a sensitivity and specificity of 90.1% (172 of 191; 95% CI: 86.0%, 94.3%) and 94.2% (24 814 of 26 349; 95% CI: 94.0%, 94.6%) while reading 80.7% (21 420 of 26 540) of the mammograms. The simulated workflow improved specificity (P = .002) and obtained a noninferior sensitivity with a margin of 5% (P < .001).

Conclusion

This deep learning model has the potential to reduce radiologist workload and significantly improve specificity without harming sensitivity.

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Complex rearrangements and oncogene amplification revealed by long-read DNA and RNA sequencing of a breast cancer cell line

Reporter: Stephen J. Williams, PhD

In a Genome Research report by Marie Nattestad et al. [1], the SK-BR-3 breast cancer cell line was sequenced using a long read single molecule sequencing protocol in order to develop one of the most detailed maps of structural variations in a cancer genome to date.  The authors detected over 20,000 variants with this new sequencing modality, whereas most of these variants would have been missed by short read sequencing.  In addition, a complex sequence of nested duplications and translocations occurred surrounding the ERBB2 (HER2) while full-length transcriptomic analysis revealed novel gene fusions within the nested genomic variants.  The authors suggest that combining this long-read genome and transcriptome sequencing results in a more comprehensive coverage of tumor gene variants and “sheds new light on the complex mechanisms involved in cancer genome evolution.”

Genomic instability is a hallmark of cancer [2], which lead to numerous genetic variations such as:

  • Copy number variations
  • Chromosomal alterations
  • Gene fusions
  • Deletions
  • Gene duplications
  • Insertions
  • Translocations

Efforts such as the Cancer Genome Atlas [3], and the International Genome Consortium (2010) use short-read sequencing technology to detect and analyze thousands of commonly occurring mutations however short-read technology has a high false positive and negative rate for detecting less common genetic structural variations {as high as 50% [4]}. In addition, short reads cannot detect variations in close proximity to each other or on the same molecule, therefore underestimating the variation number.

Methods:  The authors used a long-read sequencing technology from Pacific Biosciences (SMRT) to analyze the mutational and structural variation in the SK-BR-3 breast cancer cell line.  A split read and within-read mapping approach was used to detect variants of different types and sizes.  In general, long-reads have better alignment qualities than short reads, resulting in higher quality mapping. Transcriptomic analysis was performed using Iso-Seq.

Results: Using the SMRT long-read sequencing technology from Pacific Biosciences, the authors were able to obtain 71.9% sequencing coverage with average read length of 9.8 kb for the SK-BR-3 genome.

A few notes:

  1. Most amplified regions (33.6 copies) around the locus spanning the ERBB2 oncogene and around MYC locus (38 copies), EGFR locus (7 copies) and BCAS1 (16.8 copies)
  2. The locus 8q24.12 had the most amplifications (this locus contains the SNTB1 gene) at 69.2 copies
  3. Long-read sequencing showed more insertions than deletions and suggests an underestimate of the lengths of low complexity regions in the human reference genome
  4. Found 1,493 long read variants, 603 of which were between different chromosomes
  5. Using Iso-Seq in conjunction with the long-read platform, they detected 1,692,379 isoforms (93%) mapping to the reference genome and 53 putative gene fusions (39 of which they found genomic evidence)

A table modified from the paper on the gene fusions is given below:

Table 1. Gene fusions with RNA evidence from Iso-Seq and DNA evidence from SMRT DNA sequencing where the genomic path is found using SplitThreader from Sniffles variant calls. Note link in table is  GeneCard for each gene.

SplitThreader path

 

# Genes Distance
(bp)
Number
of variants
Chromosomes
in path
Previously observed in references
1 KLHDC2 SNTB1 9837 3 14|17|8 Asmann et al. (2011) as only a 2-hop fusion
2 CYTH1 EIF3H 8654 2 17|8 Edgren et al. (2011); Kim and Salzberg
(2011); RNA only, not observed as 2-hop
3 CPNE1 PREX1 1777 2 20 Found and validated as 2-hop by Chen et al. 2013
4 GSDMB TATDN1 0 1 17|8 Edgren et al. (2011); Kim and Salzberg
(2011); Chen et al. (2013); validated by
Edgren et al. (2011)
5 LINC00536 PVT1 0 1 8 No
6 MTBP SAMD12 0 1 8 Validated by Edgren et al. (2011)
7 LRRFIP2 SUMF1 0 1 3 Edgren et al. (2011); Kim and Salzberg
(2011); Chen et al. (2013); validated by
Edgren et al. (2011)
8 FBXL7 TRIO 0 1 5 No
9 ATAD5 TLK2 0 1 17 No
10 DHX35 ITCH 0 1 20 Validated by Edgren et al. (2011)
11 LMCD1-AS1 MECOM 0 1 3 No
12 PHF20 RP4-723E3.1 0 1 20 No
13 RAD51B SEMA6D 0 1 14|15 No
14 STAU1 TOX2 0 1 20 No
15 TBC1D31 ZNF704 0 1 8 Edgren et al. (2011); Kim and Salzberg
(2011); Chen et al. (2013); validated by
Edgren et al. (2011); Chen et al. (2013)

 

SplitThreader found two different paths for the RAD51B-SEMA6D gene fusion and for the LINC00536-PVT1 gene fusion. Number of Iso-Seq reads refers to full-length HQ-filtered reads. Alignments of SMRT DNA sequence reads supporting each of these gene fusions are shown in Supplemental Note S2.

 

 References

 

  1. Nattestad M, Goodwin S, Ng K, Baslan T, Sedlazeck FJ, Rescheneder P, Garvin T, Fang H, Gurtowski J, Hutton E et al: Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line. Genome research 2018, 28(8):1126-1135.
  2. Hanahan D, Weinberg RA: The hallmarks of cancer. Cell 2000, 100(1):57-70.
  3. Kandoth C, McLellan MD, Vandin F, Ye K, Niu B, Lu C, Xie M, Zhang Q, McMichael JF, Wyczalkowski MA et al: Mutational landscape and significance across 12 major cancer types. Nature 2013, 502(7471):333-339.
  4. Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Fritz MH et al: An integrated map of structural variation in 2,504 human genomes. Nature 2015, 526(7571):75-81.

 

Other articles on Cancer Genome Sequencing in this Open Access Journal Include:

 

International Cancer Genome Consortium Website has 71 Committed Cancer Genome Projects Ongoing

Loss of Gene Islands May Promote a Cancer Genome’s Evolution: A new Hypothesis on Oncogenesis

Identifying Aggressive Breast Cancers by Interpreting the Mathematical Patterns in the Cancer Genome

CancerBase.org – The Global HUB for Diagnoses, Genomes, Pathology Images: A Real-time Diagnosis and Therapy Mapping Service for Cancer Patients – Anonymized Medical Records accessible to

 

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Tumor Ammonia Recycling: How Cancer Cells Use Glutamate Dehydrogenase to Recycle Tumor Microenvironment Waste Products for Biosynthesis

Reporter: Stephen J. Williams, PhD

A feature of the tumorigenic process is the rewiring of the metabolic processes that provides a tumor cell the ability to grow and thrive in conditions of limiting nutrients as well as the ability to utilize waste products in salvage pathways for production of new biomass (amino acids, nucleic acids etc.) required for cellular growth and division 1-8.  A Science article from Spinelli et al. 9 (and corresponding Perspective article in the same issue by Dr. Chi V. Dang entitled Feeding Frenzy for Cancer Cells 10) describes the mechanism by which estrogen-receptor positive (ER+) breast cancer cells convert glutamine to glutamate, release ammonia  into the tumor microenvironment, diffuses into tumor cells and eventually recycle this ammonia by reductive amination of a-ketoglutarate by glutamate dehydrogenase (GDH) to produce glutamic acid and subsequent other amino acids needed for biomass production.   Ammonia can accumulate in the tumor microenvironment in poorly vascularized tumor. Thus ammonia becomes an important nitrogen source for tumor cells.

Mammalian cells have a variety of mechanisms to metabolize ammonia including

  • Glutamate synthetase (GS) in the liver can incorporate ammonia into glutamate to form glutamine
  • glutamate dehydrogenase (GDH) converts glutamate to a-ketoglutarate and ammonia under allosteric regulation (discussed in a post on this site by Dr. Larry H. Berstein; subsection Drugging Glutaminolysis)
  • the reverse reaction of GDH, which was found to occur in ER+ breast cancer cells, a reductive amination of a-ketoglutarate to glutamate11, is similar to the reductive carboxylation of a-ketoglutarate to citrate by isocitrate dehydrogenase (IDH) for fatty acid synthesis (IDH is overexpressed in many tumor types including cancer stem cells 12-15), and involved in immune response and has been developed as a therapeutic target for various cancers. IDH mutations were shown to possess the neomorphic activity to generate the oncometabolite, 2-hydroxyglutarate (2HG) 16-18. With a single codon substitution, the kinetic properties of the mutant IDH isozyme are significantly altered, resulting in an obligatory sequential ordered reaction in the reverse direction 19.

 

In the Science paper, Spinelli et al. report that ER+ breast cancer cells have the ability to utilize ammonia sources from their surroundings in order to produce amino acids and biomass as these ER+ breast cancer cells have elevated levels of GS and GDH with respect to other breast cancer histotypes.

GDH was elevated in ER+ luminal cancer cells and the quiescent epithelial cells in organoid culture

However proliferative cells were dependent on transaminases, which transfers nitrogen from glutamate to pyruvate or oxaloacetate to form a-ketoglutarate and alanine or aspartate. a-ketoglutarate is further metabolized in the citric acid cycle.

 

 

 

 

 

 

 

 

 

 

 

 

 

Figure 1.    Reductive amination and transamination reactions of glutamic acid.  Source http://www.biologydiscussion.com/organism/metabolism-organism/incorporation-of-ammonia-into-organic-compounds/50870

Spinelli et al. showed GDH is necessary for ammonia reductive incorporation into a-ketoglutarate and also required for ER+ breast cancer cell growth in immunocompromised mice.

In addition, as commented by Dr. Dang in his associated Perspectives article, (quotes indent)

The metabolic tumor microenvironment produced by resident cells, such as fibroblasts and macrophages, can create an immunosuppressive environment 20.  Hence, it will be of great interest to further understand whether products such as ammonia could affect tumor immunity or induce autophagy  (end quote indent)

 

 

 

Figure 2.  Tumor ammonia recycling.  Source:  From Chi V. Dang Feeding Frenzy for cancer cells.  Rights from RightsLink (copyright.com)

Metabolic recycling of ammonia via glutamate dehydrogenase supports breast cancer biomass

Jessica B. Spinelli1,2, Haejin Yoon1, Alison E. Ringel1, Sarah Jeanfavre2, Clary B. Clish2, Marcia C. Haigis1 *

1.      1Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA. 2.      2Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.

* *Corresponding author. Email: marcia_haigis@hms.harvard.edu

Science  17 Nov 2017:Vol. 358, Issue 6365, pp. 941-946 DOI: 10.1126/science.aam9305

Abstract

Ammonia is a ubiquitous by-product of cellular metabolism; however, the biological consequences of ammonia production are not fully understood, especially in cancer. We found that ammonia is not merely a toxic waste product but is recycled into central amino acid metabolism to maximize nitrogen utilization. In our experiments, human breast cancer cells primarily assimilated ammonia through reductive amination catalyzed by glutamate dehydrogenase (GDH); secondary reactions enabled other amino acids, such as proline and aspartate, to directly acquire this nitrogen. Metabolic recycling of ammonia accelerated proliferation of breast cancer. In mice, ammonia accumulated in the tumor microenvironment and was used directly to generate amino acids through GDH activity. These data show that ammonia is not only a secreted waste product but also a fundamental nitrogen source that can support tumor biomass.

 

 

References

1          Strickaert, A. et al. Cancer heterogeneity is not compatible with one unique cancer cell metabolic map. Oncogene 36, 2637-2642, doi:10.1038/onc.2016.411 (2017).

2          Hui, S. et al. Glucose feeds the TCA cycle via circulating lactate. Nature 551, 115-118, doi:10.1038/nature24057 (2017).

3          Mashimo, T. et al. Acetate is a bioenergetic substrate for human glioblastoma and brain metastases. Cell 159, 1603-1614, doi:10.1016/j.cell.2014.11.025 (2014).

4          Sousa, C. M. et al. Erratum: Pancreatic stellate cells support tumour metabolism through autophagic alanine secretion. Nature 540, 150, doi:10.1038/nature19851 (2016).

5          Sousa, C. M. et al. Pancreatic stellate cells support tumour metabolism through autophagic alanine secretion. Nature 536, 479-483, doi:10.1038/nature19084 (2016).

6          Commisso, C. et al. Macropinocytosis of protein is an amino acid supply route in Ras-transformed cells. Nature 497, 633-637, doi:10.1038/nature12138 (2013).

7          Hanahan, D. & Weinberg, R. A. The hallmarks of cancer. Cell 100, 57-70 (2000).

8          Hanahan, D. & Weinberg, R. A. Hallmarks of cancer: the next generation. Cell 144, 646-674, doi:10.1016/j.cell.2011.02.013 (2011).

9          Spinelli, J. B. et al. Metabolic recycling of ammonia via glutamate dehydrogenase supports breast cancer biomass. Science 358, 941-946, doi:10.1126/science.aam9305 (2017).

10        Dang, C. V. Feeding frenzy for cancer cells. Science 358, 862-863, doi:10.1126/science.aaq1070 (2017).

11        Smith, T. J. & Stanley, C. A. Untangling the glutamate dehydrogenase allosteric nightmare. Trends in biochemical sciences 33, 557-564, doi:10.1016/j.tibs.2008.07.007 (2008).

12        Metallo, C. M. et al. Reductive glutamine metabolism by IDH1 mediates lipogenesis under hypoxia. Nature 481, 380-384, doi:10.1038/nature10602 (2011).

13        Garrett, M. et al. Metabolic characterization of isocitrate dehydrogenase (IDH) mutant and IDH wildtype gliomaspheres uncovers cell type-specific vulnerabilities. Cancer & metabolism 6, 4, doi:10.1186/s40170-018-0177-4 (2018).

14        Calvert, A. E. et al. Cancer-Associated IDH1 Promotes Growth and Resistance to Targeted Therapies in the Absence of Mutation. Cell reports 19, 1858-1873, doi:10.1016/j.celrep.2017.05.014 (2017).

15        Sciacovelli, M. & Frezza, C. Metabolic reprogramming and epithelial-to-mesenchymal transition in cancer. The FEBS journal 284, 3132-3144, doi:10.1111/febs.14090 (2017).

16        Dang, L. et al. Cancer-associated IDH1 mutations produce 2-hydroxyglutarate. Nature 462, 739-744, doi:10.1038/nature08617 (2009).

17        Gross, S. et al. Cancer-associated metabolite 2-hydroxyglutarate accumulates in acute myelogenous leukemia with isocitrate dehydrogenase 1 and 2 mutations. The Journal of experimental medicine 207, 339-344, doi:10.1084/jem.20092506 (2010).

18        Ward, P. S. et al. The common feature of leukemia-associated IDH1 and IDH2 mutations is a neomorphic enzyme activity converting alpha-ketoglutarate to 2-hydroxyglutarate. Cancer cell 17, 225-234, doi:10.1016/j.ccr.2010.01.020 (2010).

19        Rendina, A. R. et al. Mutant IDH1 enhances the production of 2-hydroxyglutarate due to its kinetic mechanism. Biochemistry 52, 4563-4577, doi:10.1021/bi400514k (2013).

20        Zhang, X. et al. IDH mutant gliomas escape natural killer cell immune surveillance by downregulation of NKG2D ligand expression. Neuro-oncology 18, 1402-1412, doi:10.1093/neuonc/now061 (2016).

 

Other articles on this Open Access Journal on Cancer Metabolism Include:

 

Is the Warburg Effect the Cause or the Effect of Cancer: A 21st Century View?

 

Accumulation of 2-hydroxyglutarate is not a biomarker for malignant progression of IDH-mutated low grade gliomas

 

 

Protein-binding, Protein-Protein interactions & Therapeutic Implications [7.3]

Is the Warburg effect an effect of deregulated space occupancy of methylome?

Therapeutic Implications for Targeted Therapy from the Resurgence of Warburg ‘Hypothesis’

New Insights on the Warburg Effect [2.2]

The Inaugural Judith Ann Lippard Memorial Lecture in Cancer Research: PI 3 Kinase & Cancer Metabolism

Renal (Kidney) Cancer: Connections in Metabolism at Krebs cycle and Histone Modulation

Warburg Effect and Mitochondrial Regulation- 2.1.3

Refined Warburg Hypothesis -2.1.2

 

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Reporter: Gail S. Thornton

This article appeared on the web site of Harley Street Concierge, one of the U.K.’s leading independent providers of clinical, practical and emotion support for cancer patients. 

Cancer at Work: An Interview With Barbara Wilson

Whether you’re supporting an employee through cancer at work. Or you’re a cancer patient struggling to get the support you need. Either way, this Q and A with Barbara Wilson will help you out. Read on for a glimpse into Barbara’s personal experience with breast cancer. Find out where companies are falling short of supporting employees. Discover what you need to do if you’re feeling unsupported at work. And learn what’s unacceptable for Barbara in a modern and civilised society.

In a 2013 interview about cancer at work, you expressed amazement at “the lack of understanding there is about cancer. And what the impact is on individuals”. How would you say this has improved in the last 4 years? And what do you feel still needs to change?

There’s greater awareness and understanding about cancer at work. More organisations are aware of the difficulties people face. But many organisations don’t appreciate that recovery isn’t straightforward or quick. They also tend to rely on generic return to work policies. And these are inappropriate when it comes to supporting people recovering from cancer. A lot still depends on how far the local line manager is prepared to support an employee. And whether they’ll bend rules if need be about leave or sick pay.

You were diagnosed with breast cancer in 2005 and given the all clear in 2010. What did you learn about yourself through treatment and recovery?

 

I learned that I wasn’t immortal or superhuman! And also that life is precious and so it’s important to make the best of it. That doesn’t actually mean counting off things on your bucket list. Or living each day as if it’s your last. It’s about appreciating what you have, family, friends and the sheer joy of being alive.

“Life is precious. It’s about appreciating what you have, family, friends and the sheer joy of being alive.”

It’s a common misperception that people in remission want more family time or to travel the world. What reasons do your clients share with you for wanting to get back to work?

Yes. Before I had cancer, I remember asking a terminally ill employee why she still wanted to work. And she worked until a fortnight before her death. The simple answer is that it’s about feeling normal. Using your brain. Being with friends and colleagues rather than on your own. And losing yourself in your work. There are also financial reasons. But typically – and I can say this based on my own experience – it’s about being ‘you’ again rather than a cancer patient.

“I remember asking a terminally ill employee why she still wanted to work. And she worked until a fortnight before her death. Typically – and I can say this based on my own experience – it’s about being ‘you’ again rather than a cancer patient.”

You share tips for employers and HR professionals in this article for Macmillan. And you set out how to support a colleague during and after cancer treatment. What would you say to an employee who isn’t feeling supported by their employer or colleagues in this way?

In my experience there are two main reasons why people often aren’t supported.

1. Bosses and colleagues don’t understand the full impact of cancer treatment. They won’t understand what fatigue is or chemo brain or peripheral neuropathy. So they often expect people to get ‘back to normal’ work after 6 to 8 weeks. But recovery can take many months. This isn’t helped by the person often looking fit and well.

2. People don’t like talking about cancer at work. They feel awkward. And as a result often decide to say nothing. We advise people to be open from the outset. To understand their right to reasonable adjustments. And their responsibility to update their employer about their recovery and support needs. Employees recovering from cancer often have to take the lead. They have to guide their colleagues about the specific help they need. You can’t expect others to do it for you. It sounds wrong but that’s how it is.

“Bosses and colleagues often expect people to get ‘back to normal’ work after 6 to 8 weeks. But recovery can take many months. “

More than 100,000 people had to wait more than 2 weeks to see a cancer specialist in the UK last year. 25,153 had to wait more than 62 days to start treatment. What’s your reaction to these statistics?

It’s shocking. The worry for patients and their families during this period is totally debilitating. And on top of this it means that the cancer is growing unchecked. Where the cancer is aggressive, the delay may threaten lives. And it will certainly add to the overall costs of care. We really have to address this. It’s just not acceptable in a modern and civilised society.

“The worry for patients and their families during this period is totally debilitating. We really have to address this.”

Finally, can you tell us more about Working With Cancer?

Working With Cancer is a social enterprise and was established in June 2014. We support people affected by cancer to lead fulfilling and rewarding working lives. That means helping people to successfully return to work or remain in work. Or sometimes it’s about helping people to find work – depending on their personal needs. We work with corporate, charities and other third sector organisations to support people throughout the UK.

We coach people diagnosed with cancer to re-establish their working lives. And we train employers to understand how to manage work and cancer. We’ll advise teams about how to support a colleague affected by cancer. And we help carers juggle work whilst supporting their loved ones. Working With Cancer also helps organisations to update or improve their policies.

Barbara Wilson - Cancer at Work

About Barbara Wilson

Barbara Wilson is a senior HR professional with almost 40 years’ experience.  Roles include Group Head of Strategic HR at Catlin Group Ltd. Deputy Head of HR at Schroders Investment Management. And Chief of Staff to the Group HR Director at Barclays. After a breast cancer diagnosis, Barbara launched Working With Cancer. It’s a Social Enterprise providing coaching, training and consultancy to employers, employees, carers and health professionals.

 

For more information about Working With Cancer, click here to visit the websiteFollow this link to connect with Barbara on Twitter. Email admin@workingwithcancer.co.uk. Or call 07508 232257 or 07919 147784.

 

SOURCE

https://harleystreetconcierge.com/cancer-at-work/

Other posts on the JP Morgan 2019 Healthcare Conference on this Open Access Journal include:

2018

Top 10 Cancer Research Priorities

https://pharmaceuticalintelligence.com/2018/12/24/top-10-cancer-research-priorities/

Innovation + Technology = Good Patient Experience

https://pharmaceuticalintelligence.com/2018/12/24/innovation-technology-good-patient-experience/

2017

Inspiring Book for ALL Cancer Survivors, ALL Cancer Patients and ALL Cardiac Patients – The VOICES of Patients, Hospitals CEOs, Health Care Providers, Caregivers and Families: Personal Experience with Critical Care and Invasive Medical Procedures

https://pharmaceuticalintelligence.com/2017/10/24/inspiring-book-for-all-cancer-survivors-all-cancer-patients-and-all-cardiac-patients-the-voices-of-patients-hospitals-ceos-health-care-providers-caregivers-and-families-personal-experience-with/

2016

Funding Opportunities for Cancer Research

https://pharmaceuticalintelligence.com/2016/12/08/funding-opportunities-for-cancer-research/

2012

The Incentive for “Imaging based cancer patient’ management”

https://pharmaceuticalintelligence.com/2012/08/27/the-incentive-for-imaging-based-cancer-patient-management/

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Lesson 9 Cell Signaling:  Curations and Articles of reference as supplemental information for lecture section on WNTs: #TUBiol3373

Stephen J. Wiilliams, Ph.D: Curator

UPDATED 4/23/2019

This has an updated lesson on WNT signaling.  Please click on the following and look at the slides labeled under lesson 10

cell motility 9b lesson_2018_sjw

Remember our lessons on the importance of signal termination.  The CANONICAL WNT signaling (that is the β-catenin dependent signaling)

is terminated by the APC-driven degradation complex.  This leads to the signal messenger  β-catenin being degraded by the proteosome.  Other examples of growth factor signaling that is terminated by a proteosome-directed include the Hedgehog signaling system, which is involved in growth and differentiation as well as WNTs and is implicated in various cancers.

A good article on the Hedgehog signaling pathway is found here:

The Voice of a Pathologist, Cancer Expert: Scientific Interpretation of Images: Cancer Signaling Pathways and Tumor Progression

All images in use for this article are under copyrights with Shutterstock.com

Cancer is expressed through a series of transformations equally involving metabolic enzymes and glucose, fat, and protein metabolism, and gene transcription, as a result of altered gene regulatory and transcription pathways, and also as a result of changes in cell-cell interactions.  These are embodied in the following series of graphics.

Figure 1: Sonic_hedgehog_pathwaySonic_hedgehog_pathway

The Voice of Dr. Larry

The figure shows a modification of nuclear translocation by Sonic hedgehog pathway. The hedgehog proteins have since been implicated in the development of internal organs, midline neurological structures, and the hematopoietic system in humans. The Hh signaling pathway consists of three main components: the receptor patched 1 (PTCH1), the seven transmembrane G-protein coupled receptor smoothened (SMO), and the intracellular glioma-associated oncogene homolog (GLI) family of transcription factors.5The GLI family is composed of three members, including GLI1 (gene activating), GLI2 (gene activating and repressive), and GLI3 (gene repressive).6 In the absence of an activating signal from either Shh, Ihh or Dhh, PTCH1 exerts an inhibitory effect on the signal transducer SMO, preventing any downstream signaling from occurring.7 When Hh ligands bind and activate PTCH1, the inhibition on SMO is released, allowing the translocation of SMO into the cytoplasm and its subsequent activation of the GLI family of transcription factors.

 

And from the review of  Elaine Y. C. HsiaYirui Gui, and Xiaoyan Zheng   Regulation of Hedgehog Signaling by Ubiquitination  Front Biol (Beijing). 2015 Jun; 10(3): 203–220.

the authors state:

Finally, termination of Hh signaling is also important for controlling the duration of pathway activity. Hh induced ubiquitination and degradation of Ci/Gli is the most well-established mechanism for limiting signal duration, and inhibiting this process can lead to cell patterning disruption and excessive cell proliferation (). In addition to Ci/Gli, a growing body of evidence suggests that ubiquitination also plays critical roles in regulating other Hh signaling components including Ptc, Smo, and Sufu. Thus, ubiquitination serves as a general mechanism in the dynamic regulation of the Hh pathway.

Overview of Hedgehog signaling showing the signal termination by ubiquitnation and subsequent degradation of the Gli transcriptional factors. obtained from Oncotarget 5(10):2881-911 · May 2014. GSK-3B as a Therapeutic Intervention in Cancer

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Note that in absence of Hedgehog ligands Ptch inhibits Smo accumulation and activation but upon binding of Hedgehog ligands (by an autocrine or paracrine fashion) Ptch is now unable to inhibit Smo (evidence exists that Ptch is now targeted for degradation) and Smo can now inhibit Sufu-dependent and GSK-3B dependent induced degradation of Gli factors Gli1 and Gli2.  Also note the Gli1 and Gli2 are transcriptional activators while Gli3 is a transcriptional repressor.

UPDATED 4/16/2019

Please click on the following links for the Powerpoint presentation for lesson 9.  In addition click on the mp4 links to download the movies so you can view them in Powerpoint slide 22:

cell motility 9 lesson_SJW 2019

movie file 1:

Tumorigenic but noninvasive MCF-7 cells motility on an extracellular matrix derived from normal (3DCntrol) or tumor associated (TA) fibroblasts.  Note that TA ECM is “soft” and not organized and tumor cells appear to move randomly if  much at all.

Movie 2:

 

Note that these tumorigenic and invasive MDA-MB-231 breast cancer cells move in organized patterns on organized ECM derived from Tumor Associated (TA) fibroblasts than from the ‘soft’ or unorganized ECM derived from normal  (3DCntrl) fibroblasts

 

The following contain curations of scientific articles from the site https://pharmaceuticalintelligence.com  intended as additional reference material  to supplement material presented in the lecture.

Wnts are a family of lipid-modified secreted glycoproteins which are involved in:

Normal physiological processes including

A. Development:

– Osteogenesis and adipogenesis (Loss of wnt/β‐catenin signaling causes cell fate shift of preosteoblasts from osteoblasts to adipocytes)

  – embryogenesis including body axis patterning, cell fate specification, cell proliferation and cell migration

B. tissue regeneration in adult tissue

read: Wnt signaling in the intestinal epithelium: from endoderm to cancer

And in pathologic processes such as oncogenesis (refer to Wnt/β-catenin Signaling [7.10]) and to your Powerpoint presentation

 

The curation Wnt/β-catenin Signaling is a comprehensive review of canonical and noncanonical Wnt signaling pathways

 

To review:

 

 

 

 

 

 

 

 

 

 

 

Activating the canonical Wnt pathway frees B-catenin from the degradation complex, resulting in B-catenin translocating to the nucleus and resultant transcription of B-catenin/TCF/LEF target genes.

Fig. 1 Canonical Wnt/FZD signaling pathway. (A) In the absence of Wnt signaling, soluble β-catenin is phosphorylated by a degradation complex consisting of the kinases GSK3β and CK1α and the scaffolding proteins APC and Axin1. Phosphorylated β-catenin is targeted for proteasomal degradation after ubiquitination by the SCF protein complex. In the nucleus and in the absence of β-catenin, TCF/LEF transcription factor activity is repressed by TLE-1; (B) activation of the canonical Wnt/FZD signaling leads to phosphorylation of Dvl/Dsh, which in turn recruits Axin1 and GSK3β adjacent to the plasma membrane, thus preventing the formation of the degradation complex. As a result, β-catenin accumulates in the cytoplasm and translocates into the nucleus, where it promotes the expression of target genes via interaction with TCF/LEF transcription factors and other proteins such as CBP, Bcl9, and Pygo.

NOTE: In the canonical signaling, the Wnt signal is transmitted via the Frizzled/LRP5/6 activated receptor to INACTIVATE the degradation complex thus allowing free B-catenin to act as the ultimate transducer of the signal.

Remember, as we discussed, the most frequent cancer-related mutations of WNT pathway constituents is in APC.

This shows how important the degradation complex is in controlling canonical WNT signaling.

Other cell signaling systems are controlled by protein degradation:

A.  The Forkhead family of transcription factors

Read: Regulation of FoxO protein stability via ubiquitination and proteasome degradation

B. Tumor necrosis factor α/NF κB signaling

Read: NF-κB, the first quarter-century: remarkable progress and outstanding questions

1.            Question: In cell involving G-proteins, the signal can be terminated by desensitization mechanisms.  How is both the canonical and noncanonical Wnt signal eventually terminated/desensitized?

We also discussed the noncanonical Wnt signaling pathway (independent of B-catenin induced transcriptional activity).  Note that the canonical and noncanonical involve different transducers of the signal.

Noncanonical WNT Signaling

Note: In noncanonical signaling the transducer is a G-protein and second messenger system is IP3/DAG/Ca++ and/or kinases such as MAPK, JNK.

Depending on the different combinations of WNT ligands and the receptors, WNT signaling activates several different intracellular pathways  (i.e. canonical versus noncanonical)

 

In addition different Wnt ligands are expressed at different times (temporally) and different cell types in development and in the process of oncogenesis. 

The following paper on Wnt signaling in ovarian oncogenesis shows how certain Wnt ligands are expressed in normal epithelial cells but the Wnt expression pattern changes upon transformation and ovarian oncogenesis. In addition, differential expression of canonical versus noncanonical WNT ligands occur during the process of oncogenesis (for example below the authors describe the noncanonical WNT5a is expressed in normal ovarian  epithelia yet WNT5a expression in ovarian cancer is lower than the underlying normal epithelium. However the canonical WNT10a, overexpressed in ovarian cancer cells, serves as an oncogene, promoting oncogenesis and tumor growth.

Wnt5a Suppresses Epithelial Ovarian Cancer by Promoting Cellular Senescence

Benjamin G. Bitler,1 Jasmine P. Nicodemus,1 Hua Li,1 Qi Cai,2 Hong Wu,3 Xiang Hua,4 Tianyu Li,5 Michael J. Birrer,6Andrew K. Godwin,7 Paul Cairns,8 and Rugang Zhang1,*

A.           Abstract

Epithelial ovarian cancer (EOC) remains the most lethal gynecological malignancy in the US. Thus, there is an urgent need to develop novel therapeutics for this disease. Cellular senescence is an important tumor suppression mechanism that has recently been suggested as a novel mechanism to target for developing cancer therapeutics. Wnt5a is a non-canonical Wnt ligand that plays a context-dependent role in human cancers. Here, we investigate the role of Wnt5a in regulating senescence of EOC cells. We demonstrate that Wnt5a is expressed at significantly lower levels in human EOC cell lines and in primary human EOCs (n = 130) compared with either normal ovarian surface epithelium (n = 31; p = 0.039) or fallopian tube epithelium (n = 28; p < 0.001). Notably, a lower level of Wnt5a expression correlates with tumor stage (p = 0.003) and predicts shorter overall survival in EOC patients (p = 0.003). Significantly, restoration of Wnt5a expression inhibits the proliferation of human EOC cells both in vitro and in vivo in an orthotopic EOC mouse model. Mechanistically, Wnt5a antagonizes canonical Wnt/β-catenin signaling and induces cellular senescence by activating the histone repressor A (HIRA)/promyelocytic leukemia (PML) senescence pathway. In summary, we show that loss of Wnt5a predicts poor outcome in EOC patients and Wnt5a suppresses the growth of EOC cells by triggering cellular senescence. We suggest that strategies to drive senescence in EOC cells by reconstituting Wnt5a signaling may offer an effective new strategy for EOC therapy.

Oncol Lett. 2017 Dec;14(6):6611-6617. doi: 10.3892/ol.2017.7062. Epub 2017 Sep 26.

Clinical significance and biological role of Wnt10a in ovarian cancer. 

Li P1Liu W1Xu Q1Wang C1.

Ovarian cancer is one of the five most malignant types of cancer in females, and the only currently effective therapy is surgical resection combined with chemotherapy. Wnt family member 10A (Wnt10a) has previously been identified to serve an oncogenic function in several tumor types, and was revealed to have clinical significance in renal cell carcinoma; however, there is still only limited information regarding the function of Wnt10a in the carcinogenesis of ovarian cancer. The present study identified increased expression levels of Wnt10a in two cell lines, SKOV3 and A2780, using reverse transcription-polymerase chain reaction. Functional analysis indicated that the viability rate and migratory ability of SKOV3 cells was significantly inhibited following Wnt10a knockdown using short interfering RNA (siRNA) technology. The viability rate of SKOV3 cells decreased by ~60% compared with the control and the migratory ability was only ~30% of that in the control. Furthermore, the expression levels of β-catenin, transcription factor 4, lymphoid enhancer binding factor 1 and cyclin D1 were significantly downregulated in SKOV3 cells treated with Wnt10a-siRNA3 or LGK-974, a specific inhibitor of the canonical Wnt signaling pathway. However, there were no synergistic effects observed between Wnt10a siRNA3 and LGK-974, which indicated that Wnt10a activated the Wnt/β-catenin signaling pathway in SKOV3 cells. In addition, using quantitative PCR, Wnt10a was overexpressed in the tumor tissue samples obtained from 86 patients with ovarian cancer when compared with matching paratumoral tissues. Clinicopathological association analysis revealed that Wnt10a was significantly associated with high-grade (grade III, P=0.031) and late-stage (T4, P=0.008) ovarian cancer. Furthermore, the estimated 5-year survival rate was 18.4% for patients with low Wnt10a expression levels (n=38), whereas for patients with high Wnt10a expression (n=48) the rate was 6.3%. The results of the present study suggested that Wnt10a serves an oncogenic role during the carcinogenesis and progression of ovarian cancer via the Wnt/β-catenin signaling pathway.

Targeting the Wnt Pathway includes curations of articles related to the clinical development of Wnt signaling inhibitors as a therapeutic target in various cancers including hepatocellular carcinoma, colon, breast and potentially ovarian cancer.

 

2.         Question: Given that different Wnt ligands and receptors activate different signaling pathways, AND  WNT ligands  can be deferentially and temporally expressed  in various tumor types and the process of oncogenesis, how would you approach a personalized therapy targeting the WNT signaling pathway?

3.         Question: What are the potential mechanisms of either intrinsic or acquired resistance to Wnt ligand antagonists being developed?

 

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

Targeting the Wnt Pathway [7.11]

Wnt/β-catenin Signaling [7.10]

Cancer Signaling Pathways and Tumor Progression: Images of Biological Processes in the Voice of a Pathologist Cancer Expert

e-Scientific Publishing: The Competitive Advantage of a Powerhouse for Curation of Scientific Findings and Methodology Development for e-Scientific Publishing – LPBI Group, A Case in Point 

Electronic Scientific AGORA: Comment Exchanges by Global Scientists on Articles published in the Open Access Journal @pharmaceuticalintelligence.com – Four Case Studies

 

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Moderna Therapeutics Deal with Merck: Are Personalized Vaccines here?

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

Take aways:

  • RNA based vaccines are a cost-effective method of developing and manufacturing a personalized cancer vaccine strategy; traditional vaccine methodology has not been met with much success as a cancer therapeutic
  • Most of the older RNA vaccine technology depended on isolated dendritic cells or T cell populations and ex-vivo treatment with RNA vaccine, HOWEVER, Moderna has developed a technology that circumvents the need for ex-vivo vaccination
  • There are multiple companies involved in this new RNA strategy (Moderna, Caperna {now Moderna}, CureVac, Biontech)

From BusinessWire at http://www.businesswire.com/news/home/20160629005446/en/Merck-Moderna-Announce-Strategic-Collaboration-Advance-mRNA-Based

Merck and Moderna Announce Strategic Collaboration to Advance Novel mRNA-Based Personalized Cancer Vaccines with KEYTRUDA®(pembrolizumab) for the Treatment of Multiple Types of Cancer

Collaboration Combines Merck’s Leadership in Immuno-Oncology with Moderna’s Pioneering mRNA Vaccine Technology and Rapid Cycle Time, Small-Batch GMP Manufacturing Capabilities

KENILWORTH, N.J. & CAMBRIDGE, Mass.–(BUSINESS WIRE)–Merck (NYSE:MRK), known as MSD outside the United States and Canada, and Moderna Therapeutics today announced a strategic collaboration and license agreement to develop and commercialize novel messenger RNA (mRNA)-based personalized cancer vaccines. The collaboration will combine Merck’s established leadership in immuno-oncology with Moderna’s pioneering mRNA vaccine technology and GMP manufacturing capabilities to advance individually tailored cancer vaccines for patients across a spectrum of cancers.

“Combining immunotherapy with vaccine technology may be a new path toward improving outcomes for patients”

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Moderna and Merck will develop personalized cancer vaccines that utilize Moderna’s mRNA vaccine technology to encode a patient’s specific neoantigens, unique mutations present in that specific patient’s tumor. When injected into a patient, the vaccine will be designed to elicit a specific immune response that will recognize and destroy cancer cells. The companies believe that the mRNA-based personalized cancer vaccines’ ability to specifically activate an individual patient’s immune system has the potential to be synergistic with checkpoint inhibitor therapies, including Merck’s anti-PD-1 therapy, KEYTRUDA® (pembrolizumab). In addition, Moderna has developed a rapid cycle time, small-batch manufacturing technique that will uniquely allow the company to supply vaccines tailored to individual patients within weeks.

Under the terms of the agreement, Merck will make an upfront cash payment to Moderna of $200 million, which Moderna will use to lead all research and development efforts through proof of concept. The development program will entail multiple studies in several types of cancer and include the evaluation of mRNA-based personalized cancer vaccines in combination with Merck’s KEYTRUDA® (pembrolizumab). Moderna will also utilize the upfront payment to fund a portion of the build-out of a GMP manufacturing facility in suburban Boston for the purpose of personalized cancer vaccine manufacturing.

Following human proof of concept studies, Merck has the right to elect to make an additional undisclosed payment to Moderna. If exercised, the two companies will then equally share cost and profits under a worldwide collaboration for the development of personalized cancer vaccines. Moderna will have the right to elect to co-promote the personalized cancer vaccines in the U.S. The agreement entails exclusivity around combinations with KEYTRUDA. Moderna and Merck will each have the ability to combine mRNA-based personalized cancer vaccines with other (non-PD-1) agents.

Combining immunotherapy with vaccine technology may be a new path toward improving outcomes for patients,” said Dr. Roger Perlmutter, President, Merck Research Laboratories. “While the area of personalized cancer vaccine research has faced challenges in the past, there have been many recent advances, and we believe that working with Moderna to combine an immuno-oncology approach, using KEYTRUDA, with mRNA-based personalized cancer vaccines may have the potential to transform the treatment of cancer.”

“Our team has made significant progress since beginning our work in personalized cancer vaccines just last year. Through this collaboration with Merck, we are now well-positioned to accelerate research and development with a goal of entering the clinic in 2017, as well as to apply our unique GMP manufacturing capabilities to support the rapid production of these highly individualized vaccines,” said Stéphane Bancel, chief executive officer of Moderna. “We value our continued collaboration with Merck, and we look forward to working together to harness the potential of personalized cancer vaccines and immuno-oncology to bring a new treatment paradigm to patients.”

Merck and Moderna have an existing collaboration and license agreement focused on the discovery and development of mRNA-based infectious disease vaccines and passive immunity treatments. Moderna is also advancing its own pipeline of infectious disease vaccine candidates and currently has two phase 1 studies underway in Europe and the U.S.

About Moderna Therapeutics

Moderna is a clinical stage pioneer of messenger RNA Therapeutics™, an entirely new in vivo drug technology that produces human proteins, antibodies and entirely novel protein constructs inside patient cells, which are in turn secreted or active intracellularly. This breakthrough platform addresses currently undruggable targets and offers a potentially superior alternative to existing drug modalities for a wide range of diseases and conditions. Moderna is developing and plans to commercialize its innovative mRNA drugs through its own ventures and its strategic relationships with established pharmaceutical and biotech companies. Its current ventures are:

  • Onkaido, focused on oncology,
  • Valera, focused on infectious diseases,
  • Elpidera, focused on rare diseases, and
  • Caperna, focused on personalized cancer vaccines.

Cambridge-based Moderna is privately held and currently has strategic agreements with AstraZeneca, Alexion Pharmaceuticals and Merck. To learn more, visit www.modernatx.com.

From the Moderna Therapeutics Website

Our mRNA Platform

At Moderna, we are pioneering the development of a new class of drugs made of messenger RNA (mRNA). This novel drug platform builds on the discovery that modified mRNA can direct the body’s cellular machinery to produce nearly any protein of interest, from native proteins to antibodies and other entirely novel protein constructs that can have therapeutic activity inside and outside of cells.

Our efforts are helping Moderna and the industry to flatten the mRNA learning curve across the full breadth of competencies needed to drive the platform forward, including chemistry, mRNA biology, formulation, process development, automation and high-throughput production, quality, and Good Manufacturing Practice (GMP) manufacturing.

Drug Modalities

Building from our mRNA core expression platform, we have created a new scale of drug discovery and development that enables a series of new drug modalities. Each modality represents a distinct approach to using the mRNA platform to encode proteins that achieve a therapeutic benefit, enabling us to develop numerous drug candidates across a wide array of therapeutic areas.

Vaccines

Vaccines are substances that teach the immune system to rapidly recognize and destroy invading pathogens such as bacteria or viruses, preparing the body’s adaptive immunity for future exposure to the pathogen. Historically, vaccines have introduced immune-activating markers from pathogens into the body. Conversely, Moderna is developing mRNA-based vaccines that enable the body to produce and present immunogenic proteins to the immune system.

Moderna is also developing mRNA-based personalized cancer vaccines to prime the immune system to recognize cancer cells and mount a strong, tailored response to each individual patient’s cancer. Moderna’s technology allows for a rapid turn-around time in production of these unique mRNA vaccines.

Intracellular/Transmembrane

Many diseases are caused by defects in proteins that function inside cells. Existing methods of protein-based therapy do not allow for proteins to reach the intracellular space, and as such are unable to replace the defective, disease-causing proteins within cells. Moderna’s platform allows for the development of mRNA therapies that can stimulate production of intracellular proteins as well as transmembrane proteins. This could potentially lead to a novel approach to treating a vast array of rare genetic and other diseases caused by intracellular protein defects.

Intratumoral

Many targets for the treatment of cancer have been identified but their therapeutic potential has been limited by either the inability to access these targets, or by systemic toxicities. Moderna’s platform allows for localized expression of therapeutic proteins within the tumor microenvironment.

Secreted antibodies

Antibodies are secreted proteins that bind to and inhibit specific targets. Moderna’s platform has the potential to stimulate the body’s own cells to produce specific antibodies that can bind to cellular targets.

Secreted proteins

Proteins are large, complex molecules that have many critical functions both inside and outside of cells. Moderna’s platform stimulates cells to produce and secrete proteins that can have a therapeutic benefit through systemic exposure.

Moderna is comprised of four smaller companies, the following three are involved in their personalized immunotherapy and cancer vaccine strategy

Caperna LLC

Caperna

Caperna LLC is the fourth Moderna venture company — formed, funded and wholly-owned by Moderna — and focused exclusively on the advancement of personalized cancer vaccines.

Caperna will apply Moderna’s mRNA vaccine technology to the field of cancer vaccines, building on advances in recent years in cancer immunotherapy. Utilizing Moderna’s demonstrated engineering and process capability to synthesize over 1,000 unique novel mRNA’s per month in Moderna’s, automated, in-house productions systems. This provides the basis for a vision of rapid turnaround times that will allow Caperna’s personalized cancer vaccine, customized after tumor biopsy and sequencing to code for specific neoantigens in patients’ tumors, to be used to treat patients with aggressive tumors and high unmet need (rather than those with less aggressive tumors which can’t wait for prolonged turnaround times). Caperna will develop its personalized cancer vaccines in combination with checkpoint inhibitors that unleash the immune system and other cancer immunotherapies.

Corporate Facts

  • President: Tal Zaks, M.D., Ph.D.
  • Head of Research: Nicholas Valiante, Ph.D.
  • Head of Operations: Ted Ashburn, M.D., Ph.D.
  • Headquarters: 500 Technology Square, Cambridge, Mass.
  • Phone: 617-714-6500
  • Website: Caperna.com

 

Onkaido

Onkaido

Onkaido Therapeutics is the first Moderna venture company – formed, funded and wholly-owned by Moderna. Onkaido is focused exclusively on developing mRNA-based oncology treatments for currently undruggable targets or as a superior alternative to existing drug modalities. Onkaido is leveraging all of the tools and modalities developed at Moderna, with plans to rapidly turn mRNA science into truly novel cancer therapies that can make a real difference for patients.

Onkaido is currently focused on three therapeutic areas of oncology drug discovery and development: immuno-oncology, hepatocellular carcinoma (liver cancer) and myeloid malignancies – with programs investigating multiple targets and therapies simultaneously. Onkaido scientists are also exploring the power of mRNA technology in precision cancer pharmacology – researching areas such as tumor biology, targeting and gene silencing, driving the science toward the delivery of truly personalized cancer treatment.

Corporate Facts

  • President: Stephen Kelsey, M.D.
  • Headquarters: 500 Technology Square, Cambridge, Mass.
  • Phone: 617-714-6500
  • Website: Onkaido.com

 

Valera

Valera

Valera LLC is the second Moderna venture company — formed, funded and wholly-owned by Moderna — and focused exclusively on the advancement of vaccines and therapeutics for the prevention and treatment of viral, bacterial and parasitic infectious diseases.

The vaccines work of Valera builds on a body of preclinical research at Moderna showing the ability of modified mRNA to express viral antigens in vivo and to induce robust immune responses. Valera’s therapeutic passive immunity programs will expand on Moderna’s research using mRNA to express antibodies that bind to viral and other targets. The robust data from these programs across a range of preclinical infectious disease models, together with the inherent, rapid turn-around time in creating novel mRNA constructs, provide Valera with a potentially powerful and versatile new platform for the creation of a broad array of vaccines and passive immunity therapies.

Corporate Facts

  • President: Michael Watson, MB ChB, MRCP, AFPM
  • Chief Scientific OfficerGiuseppe Ciaramella, Ph.D.
  • Interim Chief Medical OfficerTal Zaks, M.D., Ph.D.
  • Headquarters: 500 Technology Square, Cambridge, Mass.
  • Phone: 617-714-6500
  • Website: Valeratx.com

And from http://endpts.com/neoantigens-beckon-merck-into-a-200m-cancer-collaboration-with-moderna/

Neoantigens beckon Merck into a $200M cancer collaboration with Moderna


Now that Galena has added fresh evidence that first-gen cancer vaccines make for a poor R&D program, Merck is betting $200 million upfront that the next-gen neoantigen approach to personalized cancer vaccines can succeed where all else has failed.

Merck is tying up with the mRNA specialists at Cambridge, MA-based Moderna, which has inked a long lineup of marquee partnerships. The big idea here is that each person’s cancer cells present unique “neoantigens” that can be used to tailor a cancer vaccine for each patient.

That’s a radical idea that has gained considerable steam in recent months, with Gritstone and Neon Therapeutics — paired now with Bristol-Myers on Opdivo — rounding up significant venture cash. Biotech billionaire Patrick Soon-Shiong has also jumped into the game, including it in its growing slate of cancer R&D work in a group of startups.

Moderna says it has already set up a manufacturing system that can be used to create these personalized vaccines in a matter of weeks. And Merck will use the partnership to advance new combination therapies that include its checkpoint inhibitor Keytruda.

The way the deal works, Moderna notes in its statement, is that Merck can step up after it sees some evidence in humans that the tech is working as planned. After human proof-of-concept, if Merck wants to opt in they can pay a significant milestone and then both companies can share the cost on Phase III and commercializations, profiting equally.Moderna CEO Stéphane Bancel says they can jump into the clinic next year.

The deal marks another rare pact by Merck R&D chief Roger Perlmutter, who’s been carefully focused on making Keytruda a foundation franchise that can sustain the company for years to come. While Merck has been a couple of steps behind Bristol-Myers in gaining market share, Perlmutter’s not settling for a second place finish.

“Combining immunotherapy with vaccine technology may be a new path toward improving outcomes for patients,” said Perlmutter, president, Merck Research Laboratories. “While the area of personalized cancer vaccine research has faced challenges in the past, there have been many recent advances, and we believe that working with Moderna to combine an immuno-oncology approach, using KEYTRUDA, with mRNA-based personalized cancer vaccines may have the potential to transform the treatment of cancer.”

From FierceBiotech on failure of Galena’s breast cancer vaccine trial

Galena plummets into microcap territory on Phase III breast cancer vaccine trial halt

Immunother Cancer. 2015; 3: 26.
Published online 2015 Jun 16. doi:  10.1186/s40425-015-0068-y
PMCID: PMC4468959

Self-adjuvanted mRNA vaccination in advanced prostate cancer patients: a first-in-man phase I/IIa study

Klinikum rechts der Isar der Technischen Universität München, Munich, Germany
CureVac GmbH, Paul-Ehrlich-Str. 15, Tuebingen, 72076 Germany
Charité University Hospital Berlin, Berlin, Germany
University Hospital Freiburg, Freiburg, Germany
Universitäty Hospital Essen, Essen, Germany
San Raffaele Scientific Institute, Milan, Italy
University Hospital of the Johannes-Gutenberg-University Mainz, Mainz, Germany
Ortenau Klinikum Offenburg-Gengenbach, Offenburg, Germany
University Hospital Göttingen, Göttingen/University Hospital Mannheim, Mannheim, Germany
University Hospital Schleswig-Holstein Campus Luebeck, Luebeck, Germany
Rippin-Consulting, Solingen, Germany
University Hospital Tuebingen, Tuebingen, Germany
Hubert Kübler, ed.nehcneum-ut.zrl@relbeuK.H.
corresponding authorCorresponding author.
#Contributed equally.

Abstract

Background

CV9103 is a prostate-cancer vaccine containing self-adjuvanted mRNA (RNActive®) encoding the antigens PSA, PSCA, PSMA, and STEAP1. This phase I/IIa study evaluated safety and immunogenicity of CV9103 in patients with advanced castration-resistant prostate-cancer.

Methods

44 Patients received up to 5 intra-dermal vaccinations. Three dose levels of total mRNA were tested in Phase I in cohorts of 3–6 patients to determine a recommended dose. In phase II, 32 additional patients were treated at the recommended dose. The primary endpoint was safety and tolerability, the secondary endpoint was induction of antigen specific immune responses monitored at baseline and at weeks 5, 9 and 17.

Results

The most frequent adverse events were grade 1/2 injection site erythema, injection site reactions, fatigue, pyrexia, chills and influenza-like illness. Possibly treatment related urinary retention occurred in 3 patients. The recommended dose was 1280 μg. A total of 26/33 evaluable patients treated at 1280 μg developed an immune response, directed against multiple antigens in 15 out of 33 patients. One patient showed a confirmed PSA response. In the subgroup of 36 metastatic patients, the Kaplan-Meier estimate of median overall survival was 31.4 months [95 % CI: 21.2; n.a].

Conclusions

The self-adjuvanted RNActive® vaccine CV9103 was well tolerated and immunogenic.

The technology is a versatile, fast and cost-effective platform allowing for creation of vaccines. The follow-up vaccine CV9104 including the additional antigens prostatic acid phosphatase (PAP) and Muc1 is currently being tested in a randomized phase IIb trial to assess the clinical benefit induced by this new vaccination approach.

SOURCE

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4468959/

Other articles in the Open Access Journal on Cancer Vaccines Include:

Cancer Vaccines: Targeting Cancer Genes for Immunotherapy – A Conference by Keystone Symposia on Molecular and Cellular Biology

AACR2016 – Cancer immunotherapy

Aduro Biotech Phase II Pancreatic Cancer Trial CRS-207 plus cancer vaccine GVAX Fails

Cases in Biotech Entrepreneurship: Selective Start Ups in 2016

at #JPM16 – Moderna Therapeutics turns away an extra $200 million: with AstraZeneca (collaboration) & with Merck ($100 million investment)

 

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How cancer metastasis occurs

Larry H. Bernstein, MD, FCAP, Curator

LPBI

 

How Cancer Cells Slide along Narrow Path to Metastasis

http://www.genengnews.com/gen-news-highlights/how-cancer-cells-slide-along-narrow-path-to-metastasis/81252674/

In tumors, abnormal protein-fiber environments and genetic perturbations conspire to give rise to metastatic behavior. In this looking-glass world, cells that bump into each other do not halt and reverse direction, as they ordinarily would. Instead, they slide around each other, enhancing migratory potential and bringing to mind the portmanteau “slithy,” which Lewis Carroll invented to describe the behavior of some of his imaginary creatures.

Slithy cancer cells do gyre and gimble in the tumor microenvironment, a looking-glass world in which abnormal protein-fiber scaffolds and genetic perturbations coincide, creating conditions that promote metastasis. Some cancer cells manage to circumnavigate or slide around other cells on protein fibers, and these cells can take relatively straightforward paths out of a primary tumor. Other cells, however, are more likely to turn back upon encountering other cells. They exit tumors less efficiently.

To understand how some cancer cells migrate more efficiently than others, researchers based at Northeastern University undertook a biophysical study. They developed a model environment that mimics protein fibers. First they stamped stripes of a protein called fibronectin on glass plates, making sure to represent various widths. Then they deposited the cells—alternately hundreds of breast cancer cells and hundreds of normal cells—on these fiber­like stripes and used a microscope with time-lapse capabilties to observe and quantify their behavior.

On fibers that were 6 or 9 microns wide—the typical size of fibers in tumors—half the breast cancer cells elongated and slid around the cells they collided with. Conversely, 99% of the normal breast cells did an about face.

To under­stand what gave the cancer cells this remarkable agility, the Northeastern researchers, led by Anand Asthagiri, explored the influence of fiber widths and genetic perturbations. They presented their results April 26 in the Biophysical Journal, in an article entitled, “Regulators of Metastasis Modulate the Migratory Response to Cell Contact under Spatial Confinement.”

“Downregulating the cell–cell adhesion protein, E-cadherin, enables MCF-10A cells to slide on narrower micropatterns; meanwhile, introducing exogenous E-cadherin in metastatic MDA-MB–231 cells increases the micropattern dimension at which they slide,” wrote the article’s authors.

This finding led the Northeastern team to consider the characteristic fibrillar dimension (CFD) at which effective sliding is achieved as a metric of sliding ability under spatial confinement.

“Using this metric, we show that metastasis-promoting genetic perturbations enhance cell sliding and reduce CFD,” the article’s authors continued. “Activation of ErbB2 combined with downregulation of the tumor suppressor and cell polarity regulator, PARD3, reduced the CFD, in agreement with their cooperative role in inducing metastasis in vivo. The CFD was further reduced by a combination of ErbB2 activation and transforming growth factor β stimulation, which is known to enhance invasive behavior.”

Asthagiri’s system is relatively easy to construct and suited for rapid imaging—two qualities that make it an excellent candidate for screening new cancer drugs. Pharmaceutical companies could input the drugs along with the cancer cells and mea­sure how effectively they inhibit sliding.

In the future, the system could also alert cancer patients and clinicians before metastasis starts. Studies with patients have shown that the structure of a tumor’s protein-fiber scaffolding can indicate how far the disease has progressed. The researchers found that certain aggressive genetic mutations enabled cells to slide on very narrow fibers, whereas cells with milder mutations would slide only when the fibers got much wider. Clinicians could biopsy the tumor and mea­sure the width of the fibers to see if that danger point were approaching. “We can start to say, ‘If these fibers are approaching X microns wide, it’s urgent that we hit certain path­ways with drugs,” said Asthagiri.

Questions, of course, remain. Do other types of cancer cells also have the ability to slide? What additional genes play a role?

Next steps, says Asthagiri, include expanding their fiber­like stripes into three-dimensional models that more closely represent the fibers in actual tumors and testing cancer and normal cells together. “There are so many types of cells in a tumor environment—immune cells, blood cells, and so on,” he noted. “We want to better emulate what’s hap­pening in the body rather than in isolated cells interacting on a platform.”

 

Regulators of Metastasis Modulate the Migratory Response to Cell Contact under Spatial Confinement.

The breast tumor microenvironment (TMEN) is a unique niche where protein fibers help to promote invasion and metastasis. Cells migrating along these fibers are constantly interacting with each other. How cells respond to these interactions has important implications. Cancer cells that circumnavigate or slide around other cells on protein fibers take a less tortuous path out of the primary tumor; conversely, cells that turn back upon encountering other cells invade less efficiently. The contact response of migrating cancer cells in a fibrillar TMEN is poorly understood. Here, using high-aspect ratio micropatterns as a model fibrillar platform, we show that metastatic cells overcome spatial constraints to slide effectively on narrow fiber-like dimensions, whereas nontransformed MCF-10A mammary epithelial cells require much wider micropatterns to achieve moderate levels of sliding. Downregulating the cell-cell adhesion protein, E-cadherin, enables MCF-10A cells to slide on narrower micropatterns; meanwhile, introducing exogenous E-cadherin in metastatic MDA-MB-231 cells increases the micropattern dimension at which they slide. We propose the characteristic fibrillar dimension (CFD) at which effective sliding is achieved as a metric of sliding ability under spatial confinement. Using this metric, we show that metastasis-promoting genetic perturbations enhance cell sliding and reduce CFD. Activation of ErbB2 combined with downregulation of the tumor suppressor and cell polarity regulator, PARD3, reduced the CFD, in agreement with their cooperative role in inducing metastasis in vivo. The CFD was further reduced by a combination of ErbB2 activation and transforming growth factor β stimulation, which is known to enhance invasive behavior. These findings demonstrate that sliding is a quantitative property and a decrease in CFD is an effective metric to understand how multiple genetic hits interact to change cell behavior in fibrillar environments. This quantitative framework sheds insights into how genetic perturbations conspire with fibrillar maturation in the TMEN to drive the invasive behavior of cancer cells.

sjwilliamspa

There was a nice paper a few years ago by Dr. Edna Cukerman from Fox Chase showing how tumor cells slid down on fiber tracks generated from tumor stromal cells and how this pattern of movement is not as random as one would think. if extracellular matrix was generated from normal stromal cells you would not find athis type of coordinated movement.

 

 

Fatty acid oxidation disruption: a therapeutic alternative for triple negative breast cancer

Hormone therapy is ineffective against triple negative breast cancers (TNBC) as they lack HER2, Estrogen, and Progesterone receptors. Therefore new targetable pathways are needed to halt the cancer’s progression. Researchers at UCSF have outlined a means of treating TNBC through disruption of fatty acid oxidation (FAO). The pathway was first revealed as a potential target through metabolomics and gene signatures, identifying upregulated FAO intermediates in MYC-overexpressing TNBC samples. Considering the location, in the proximity of adipose-rich mammary glands, breast cancer FAO dependence pathway seemed to be a logical pathway. Subsequent inhibition of FAO with etomixir , an inhibitor of a major enzyme carnitine palmitoyltransferase 1 (CPT1) in the FAO pathway, lead to dramatic decreases in ATP production in MYC-overexpressing cell lines. Although a decrease in proliferation of cells in culture was observed viability remained unchanged. However, further testing of etomixir in vivo within patient derived xenograft models increased success of FAO disruption with a 4 to 6-fold decrease in relative tumor volume. The differential performance between in vitro and in vivo treatments indicates a need to recapitulate the actual tumor environment when studying metabolic manipulation regimens.

Camarda, et. al. Inhibition of fatty acid oxidation as a therapy for MYC-overexpressing triple-negative breast cancer.  Nature Medicine   

Inhibition of fatty acid oxidation as a therapy for MYC-overexpressing triple-negative breast cancer

Roman CamardaAlicia Y ZhouRebecca A Kohnz,….,Daniel K Nomura & Andrei Goga
Nature Medicine22,427–432(2016)
       
              http://dx.doi.org:/10.1038/nm.4055

Expression of the oncogenic transcription factor MYC is disproportionately elevated in triple-negative breast cancer (TNBC), as compared to estrogen receptor–, progesterone receptor– or human epidermal growth factor 2 receptor–positive (RP) breast cancer1, 2. We and others have shown that MYC alters metabolism during tumorigenesis3, 4. However, the role of MYC in TNBC metabolism remains mostly unexplored. We hypothesized that MYC-dependent metabolic dysregulation is essential for the growth of MYC-overexpressing TNBC cells and may identify new therapeutic targets for this clinically challenging subset of breast cancer. Using a targeted metabolomics approach, we identified fatty acid oxidation (FAO) intermediates as being dramatically upregulated in a MYC-driven model of TNBC. We also identified a lipid metabolism gene signature in patients with TNBC that were identified from The Cancer Genome Atlas database and from multiple other clinical data sets, implicating FAO as a dysregulated pathway that is critical for TNBC cell metabolism. We found that pharmacologic inhibition of FAO catastrophically decreased energy metabolism in MYC-overexpressing TNBC cells and blocked tumor growth in a MYC-driven transgenic TNBC model and in a MYC-overexpressing TNBC patient–derived xenograft. These findings demonstrate that MYC-overexpressing TNBC shows an increased bioenergetic reliance on FAO and identify the inhibition of FAO as a potential therapeutic strategy for this subset of breast cancer.

 

3 Dimensional Ex-Vivo for In-situ Tumor Growth

Brain tumors are both difficult to treat and hard to study because of the organ they affect. The structure of the brain is extremely sensitive to alterations. Until recently the study of architectural alterations and their effects was mostly restricted to in vivo experiments. Typical culturing of brain tissue requires disaggregation and manipulation into a 2-dimensional format, losing any anatomically relevant structure. To study the in situ brain structure, a new technique has been described by researchers from the University of Erlangen-Nürnberg. By carefully sectioning the brains of 4 day-old mice and placing them on a 0.4 uM pore-size transwell membrane 6 well plate insert within required culture medium, they were able to study the endogenous structure under varying conditions. They injected astrocytes or glioma cells with a micropipette into the slices, and investigated the structural changes brain tumors effect in their environment. Termed the Vascular Organotypic Glioma Impact Model (VOGIM), it revealed all the characteristic pathological alterations normally associated with the disease in vivo such as tumor size and borders, vessel length, vessel junctions, and vessel branches, microglia, cell survival, and neuronal modifications. As this method allows for live cell fluorescent observation, they employed the technique to observe cultures treated with the chemotherapeutic Temozolamide (TMZ, Temodal/Temcad®). Indeed they found reduced tumor growth in treatment groups vs controls, but also revealed surprising reduction in microglial cells in the peritumoral region. Additionally, they were able to observe the lack of response TMZ elicited from microglial in healthy regions of the tissue, despite its overall reduction in vascularization towards normal levels. The VOGIM technique allows for ex vivo study of brain tissue requiring three dimensional measurements, but may also be extended to other tissues with unique morphology such as kidney, liver, and intestine.

Ghoochani, et al. (December, 2015) A versatile ex vivo technique for assaying tumor angiogenesis and microglia in the brain ONCOTARGET

 

A versatile ex vivo technique for assaying tumor angiogenesis and microglia in the brain

Ali Ghoochani1, Eduard Yakubov1, Tina Sehm1, Zheng Fan1, Stefan Hock1, Michael Buchfelder1, Ilker Y. Eyüpoglu1,*, Nicolai Savaskan1,*
http://dx.doi.org:/10.18632/oncotarget.6550      PDF |  HTML

Primary brain tumors are hallmarked for their destructive activity on the microenvironment and vasculature. However, solely few experimental techniques exist to access the tumor microenvironment under anatomical intact conditions with remaining cellular and extracellular composition. Here, we detail an ex vivo vascular glioma impact method (VOGIM) to investigate the influence of gliomas and chemotherapeutics on the tumor microenvironment and angiogenesis under conditions that closely resemble the in vivo situation. We generated organotypic brain slice cultures from rats and transgenic mice and implanted glioma cells expressing fluorescent reporter proteins. In the VOGIM, tumor-induced vessels presented the whole range of vascular pathologies and tumor zones as found in human primary brain tumor specimens. In contrast, non-transformed cells such as primary astrocytes do not alter the vessel architecture. Vascular characteristics with vessel branching, junctions and vessel length are quantitatively assessable as well as the peritumoral zone. In particular, the VOGIM resembles the brain tumor microenvironment with alterations of neurons, microglia and cell survival. Hence, this method allows live cell monitoring of virtually any fluorescence-reporter expressing cell. We further analyzed the vasculature and microglia under the influence of tumor cells and chemotherapeutics such as Temozolamide (Temodal/Temcad®). Noteworthy, temozolomide normalized vasculare junctions and branches as well as microglial distribution in tumor-implanted brains. Moreover, VOGIM can be facilitated for implementing the 3Rs in experimentations. In summary, the VOGIM represents a versatile and robust technique which allows the assessment of the brain tumor microenvironment with parameters such as angiogenesis, neuronal cell death and microglial activity at the morphological and quantitative level.

 

 

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