Posts Tagged ‘Cancer stem cell’

Are CXCR4 Antagonists Making a Comeback in Cancer Chemotherapy?

Reporter: Stephen J. Williams, Ph.D.

Biospace News reported that Massachusetts based X4 Pharmaceuticals is using $34B to launch two clinical trials on its CXCR4 inhibitor X4P-001 in refractory clear cell renal cell carcinoma and refractory epithelial ovarian cancer.

The full report is below:

X4 Pharma Uses $37.5 Million to Push Cancer Therapies into Human Trials


December 14, 2015
By Alex Keown, Breaking News Staff

CAMBRIDGE, Mass. – Massachusetts based X4 Pharmaceuticals is beginning human trials for its oncology program using CXCR4 inhibitors, the Boston Business Journal reported this morning.

After spending years in stealth mode, the company, helmed by former Genzyme executives, is launching two clinical two clinical studies initiating in 2016 in refractory clear cell renal cell carcinoma and refractory epithelial ovarian cancer with its lead drug candidate, X4P-001.

The company’s pipeline is based on drug compounds that originate from a portfolio of oral CXCR4 inhibitors exclusively licensed from Sanofi (SNY), X4 said in a statement. Inhibition of CXCR4, a receptor over-expressed in many cancers, is designed to block non-cancerous immuno-suppressive and pro-angiogenic cells from populating the tumor, thereby disrupting the cancer microenvironment and restoring normal immune surveillance functions. The novel mechanism of CXCR4 inhibition increases the ability of T-Cells to track and destroy cancer. X4 is leveraging its CXCR4 research against past experience working with Genzyme’s plerixafor, which is also a CXCR4 blocker.

In an interview with the Journal, Paula Ragan, X4’s chief executive officer, said the CXCR4 protein “acts as a beacon to attract cells to surround a tumor, effectively hiding the tumor from the body’s T cells that would otherwise destroy them.” Developing a therapy to block the protein will prevent the tumors from hiding and allow it to be treated.

Ragan said the Phase Ia trial for X4P-001 will test safety and dosage in a small trial of about 20 people, the Journal reported. If all goes well the company would start a Phase 2a trial by the end of 2016 in around 50 or 60 patients, the Journal said.

In September, Ragan said a CXCR4 antagonist could potentially be paired with promising oncology drugs like Merck & Co. (MRK)’s Keytruda, or Bristol-Myers Squibb (BMY)’s Opdivo. Keytruda has been shown to be effective in treating patients with three types of cancer, melanoma, lung cancer and mesothelioma. Opdivo is a treatment of patients with metastatic squamous non-small cell lung cancer (NSCLC) with progression on or after platinum-based chemotherapy.

The cytokines and cytokine receptors have been investigated before for their utility as a chemotherapeutic target as they are highly expressed on tumors and promote metastasis. The general idea was that tumor cells secrete cytokines which promote their growth and metastases and attract immune cells which also secrete growth-promoting cytokines. Many tumor types have shown increased expression of these cytokines and cytokine receptors. However only some development efforts have shown promise, there have been no approved drugs in this class. As written in a previous post (Tumor Associated Macrophages: The Double-Edged Sword Resolved?), there could be many biological reasons for this, as well as difficulties in interpreting preclinical results in immunocompromised mice.

CXCR4: from the review by Ori Wald, Oz M. Shapira, Uzi Izha


Source: Wald O, Shapira OM, Izhar U. CXCR4/CXCL12 Axis in Non Small Cell Lung Cancer (NSCLC) Pathologic Roles and Therapeutic Potential. Theranostics 2013; 3(1):26-33. doi:10.7150/thno.4922. Available from


Chemokines, a family of 48 chemotactic cytokines interact with their 7 transmembrane G-protein-coupled receptors to guide immune cell trafficking in the body under both physiologic and pathologic conditions (20, 21). Tumor cells, which express a relatively restricted repertoire of chemokine and chemokine receptors, utilize and manipulate the chemokine system in a manner that benefits both local tumor growth and distant dissemination (20, 22, 23). In the tumor microenvironment autocrine and paracrine chamokine/chemokine receptor loops interact to promote tumor cell survival and growth, and also to enhance tumor neo-angiogenesis (20, 22, 23). At distant sites, it is the tissue-produced chemokine which guide/attracts the metastasis of chemokine receptor expressing tumor cells (20).

Among the 19 chemokine receptors, CXCR4 is the receptor most widely expressed by malignant tumors and whose role in tumor biology is most thoroughly studied (20). The chemokine CXCL12 is the sole ligand of CXCR4 and the majority of research that focus on the role of CXCR4 in cancer relates to this chemokine/chemokine receptor pair (24, 25). Nevertheless, in 2006 another receptor for CXCL12 was identified and named CXCR7 (26). CXCR7 is expressed during embriogenesis, angiogenesis and in various malignant tissues including NSCLC. CXCR7 is thought to act in part as a scavenger of CXCL12 however additional functions for this receptor have also been reported (2628). In distinct form CXCR4, CXCR7 binds not only CXCL12 but also the chemokine CXCL11 (26, 27). Moreover, the signaling cascades that are generated upon binding of CXCL12 to CXCR4 or CXCR7 vary at least partly, depending on which of the receptors is engaged (26, 27). This review focuses mainly on data collected regarding the expression and function of CXCR4 in NSCLC, nevertheless it is important to keep in mind that whenever CXCL12 is mentioned the effects related to its expression may be attributed in part to CXCR7 expression and function.

Relative to normal cells in the tumor’s tissue of origin, malignant cells often over express CXCR4, this phenotype can be induced by multiple oncogenic alternations and appears to promote tumor cell survival, proliferation, invasion and metastasis (20, 2935).





Potential roles for CXCR4/CXCL12 in NSCLC. NSCLC tumor cells express CXCR4 and produce CXCL12. Tumor expressed CXCR4 guides metastatic spread to sights such as the brain, bone marrow and liver that express high levels of CXCL12. In addition, CXCR4/CXCL12 interactions act locally in autocrine and paracrine manners to enhance primary tumor growth and to alter its inflammatory milieu. Tumor and tumor microenvironment secreted CXCL12 enhance tumor cell survival and growth and may also guide trafficking of immune and bone marrow derived cells into the tumor microenvironment. Furthermore, alternations in the tumor microenvironment result from the stimulation of tumor cells with CXCL12 that in turn enhance the production of additional chemokines such as the pro-inflammatory and pro-proliferative chemokine CCL20) pro-angiogenic and pro-proliferative chemokine (CXCL1 – IL-8). Figure from Wald O, Shapira OM, Izhar U. CXCR4/CXCL12 Axis in Non Small Cell Lung Cancer (NSCLC) Pathologic Roles and Therapeutic Potential. Theranostics 2013; 3(1):26-33. doi:10.7150/thno.4922. Available from

For further reference on CXCR4 and development of CXCR4 inhibitors please see the following references:

  1. Peled A, Wald O, Burger J. Development of novel CXCR4-based therapeutics. Expert Opin Investig Drugs. 2012Mar;21(3):341-53
  2. Balkwill FR. The chemokine system and cancer. J Pathol. 2012Jan;226(2):148-57
  3. Burger JA, Kipps TJ. CXCR4: a key receptor in the crosstalk between tumor cells and their microenvironment. Blood. 2006Mar1;107(5):1761-7
  4. Burger JA, Peled A. CXCR4 antagonists: targeting the microenvironment in leukemia and other cancers. Leukemia. 2009Jan;23(1):43-52
  5. Otsuka S, Bebb G. The CXCR4/SDF-1 chemokine receptor axis: a new target therapeutic for non-small cell lung cancer. J Thorac Oncol. 2008Dec;3(12):1379-83


Current CXCR4 inhibitors in development


Figure. Structures of Representative Small Molecule CXCR4 Antagonists and CXCL12 Inhibitors. From JJ Zariek et al. Fragment-Based Optimization of Small Molecule CXCL12 Inhibitors for Antagonizing the CXCL12/CXCR4 Interaction. Curr Top Med Chem. 2012; 12(24): 2727–2740.


A Phase 1 Trial of LY2510924, a CXCR4 Peptide Antagonist, in Patients with Advanced Cancer

This manuscript reports the results of a phase I study designed to evaluate the safety and tolerability of the C-X-C motif receptor 4 (CXCR4) inhibitor LY2510924 in patients with advanced cancer. LY2510924 is a peptide antagonist, which blocks stromal cell-derived factor-1 (SDF-1) from CXCR4 binding. CXCR4 is often overexpressed in many cancers and involved in the metastasis of solid tumors. LY2510924 was tolerated with mostly Grade 1/2 adverse events, revealed favorable pharmacokinetics, and demonstrated evidence of target engagement as indicated by dose dependent increases in CD34+ cells.

Anti-CXCR4 (BMS-936564) Alone and in Combination With Lenalidomide/Dexamethasone or Bortezomib/Dexamethasone in Relapsed/Refractory Multiple Myeloma

The purpose of this study is to determine 1) the safety and tolerability of multiple intravenous doses of anti-CXCR4 (BMS-936564) as monotherapy and as combination, and 2) the maximum tolerated dose (MTD) of BMS-936564 in combination with Lenalidomide/Dexamethasone or Bortezomib/Dexamethasone in subjects with relapsed or refractory multiple myeloma.


Novel CXCR4 Antagonist BL-8040 Enters Clinical Testing for CML – See more at:


Other posts on this Open Access Journal on CXCR4 and Chemokines in Cancer Include

Assessing effects of antimetastatic treatment

Understanding the Stem Cell Niche: A Webinar by The Scientist

Protein regulator of HIV replication

Immunotherapy in Cancer: A Series of Twelve Articles in the Frontier of Oncology by Larry H Bernstein, MD, FCAP

Humanized Mice May Revolutionize Cancer Drug Discovery

Tumor Associated Macrophages: The Double-Edged Sword Resolved?









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Reporter: Aviva Lev-Ari, PhD, RN


Researchers have identified a transcription factor, known as ZEB1, that is capable of converting non-aggressive basal-type cancer cells into highly malignant, tumor-forming cancer stem cells. [Press release from the Whitehead Institute for Biomedical Research discussing online prepublication in Cell]

Whitehead Institute is a world-renowned non-profit research institution dedicated to improving human health through basic biomedical research.
Wholly independent in its governance, finances, and research programs, Whitehead shares a close affiliation with Massachusetts Institute of Technology
through its faculty, who hold joint MIT appointments.

Cells from basal cancers are able to switch relatively easily into cancer stem cell (CSC) state, unlike luminal breast cancer cells, which tend to remain in the non-CSC state. The gene ZEB1 is critical for this conversion. The difference in ZEB1’s effects is due to the way the gene is marked in the two types of cancers. In luminal breast cancer cells, the ZEB1 gene is occupied with modifications that shut it down. But in basal breast cancer cells, ZEB1’s state is more tenuous, with repressing and activating markers coexisting on the gene. When these cells are exposed to certain signals, including those from TGFß, the repressive marks are removed and ZEB1 is expressed, thereby converting the basal non-CSCs into CSCs.


Diagram of the mechanism cancer cells use to convert into cancer stem cells

Cells from basal cancers are able to switch relatively easily into cancer stem cell (CSC) state, unlike luminal breast cancer cells, which tend to remain in the non-CSC state. The gene ZEB1 is critical for this conversion. The difference in ZEB1’s effects is due to the way the gene is marked in the two types of cancers. In luminal breast cancer cells, the ZEB1 gene is occupied with modifications that shut it down. But in basal breast cancer cells, ZEB1’s state is more tenuous, with repressing and activating markers coexisting on the gene. When these cells are exposed to certain signals, including those from TGFß, the repressive marks are removed and ZEB1 is expressed, thereby converting the basal non-CSCs into CSCs.

JULY 3, 2013


CAMBRIDGE, Mass. – In a discovery that sheds new light on the aggressiveness of certain breast cancers, Whitehead Institute researchers have identified a transcription factor, known as ZEB1, that is capable of converting non-aggressive basal-type cancer cells into highly malignant, tumor-forming cancer stem cells (CSCs). Intriguingly, luminal breast cancer cells, which are associated with a much better clinical prognosis, carry this gene in a state in which it seems to be permanently shut down.

The researchers, whose findings are published this week in the journal Cell, report that the ZEB1 gene is held in a poised state in basal non-CSCs, such that it can readily respond to environmental cues that consequently drive those non-CSCs into the dangerous CSC state. Basal-type breast carcinoma is a highly aggressive form of breast cancer. According to a 2011 epidemiological study, the 5-year survival rate for patients with basal breast cancer is 76%, compared with a roughly 90% 5-year survival rate among patients with other forms of breast cancer.

“We may have found a root source, maybe the root source, of what ultimately determines the destiny of breast cancer cells—their future benign or aggressive clinical behavior,” says Whitehead Founding Member Robert Weinberg, who is also a professor of biology at MIT and Director of the MIT/Ludwig Center for Molecular Oncology.

Transcription factors are genes that control the expression of other genes, and therefore have a significant impact on cell activities. In the case of ZEB1, it has an important role in the so-called epithelial-to-mesenchymal transition (EMT), during which epithelial cells acquire the traits of mesenchymal cells. Unlike the tightly-packed epithelial cells that stick to one another, mesenchymal cells are loose and free to move around a tissue. Previous work in the Weinberg lab showed that adult cancer cells passing through an EMT are able to self-renew and to seed new tumors with high efficiency, hallmark traits of CSCs.

Other earlier work led by Christine Chaffer, a postdoctoral researcher in the Weinberg lab, demonstrated that cancer cells are able to spontaneously become CSCs. Now Chaffer and Nemanja Marjanovic have pinpointed ZEB1, a key player in the EMT, as a gene critical for this conversion in breast cancer cells.

Breast cancers are categorized into at least five different subgroups based on their molecular profiles. More broadly these groups can be subdivided into the less aggressive ‘luminal’ subgroup or more aggressive ‘basal’ subgroup. The aggressive basal-type breast cancers often metastasize, seeding new tumors in distant parts of the body. Patients with basal breast cancer generally have a poorer prognosis than those with the less aggressive luminal-type breast cancer.

Chaffer and Marjanovic, a former research assistant in the Weinberg lab, studied non-CSCs from luminal- and basal-type cancers and determined that cells from basal cancers are able to switch relatively easily into CSC state, unlike luminal breast cancer cells, which tend to remain in the non-CSC state.

The scientists determined that the difference in ZEB1’s effects is due to the way the gene is marked in the two types of cancers. In luminal breast cancer cells, the ZEB1 gene is occupied with modifications that shut it down. But in basal breast cancer cells, ZEB1’s state is more tenuous, with repressing and activating markers coexisting on the gene. When these cells are exposed to certain signals, including those from TGFß, the repressive marks are removed and ZEB1 is expressed, thereby converting the basal non-CSCs into CSCs.

So what does this new insight mean for treating basal breast cancer?

“Well, we know that these basal breast cancer cells are very plastic and we need to incorporate that kind of thinking into treatment regimes,” says Chaffer. “As well as targeting cancer stem cells, we also need to think about how we can prevent the non-cancer stem cells from continually replenishing the pool of cancer stem cells. For example, adjuvant therapies that inhibit this type of cell plasticity may be a very effective way to keep metastasis at bay.”

Marjnaovic agrees but cautions that the model may not be applicable for every cancer.

“This is an example of how adaptable cancer cells can be,,” says Marjanovic, who is currently a research assistant at the Broad Institute. “We have yet to determine if ZEB1 plays a similar role in all cancer types, but the idea that cancer cells reside in a poised state that enables them to adapt to changing environments may be a mechanism used by many cancers to increase their aggressiveness.”


This work is supported the Advanced Medical Research Foundation (AMRF), Breast Cancer Research Foundation, and National Institutes of Health (NIH) grants HG002668 and CA146445.

Written by Nicole Giese Rura

* * *

Robert Weinberg’s primary affiliation is with Whitehead Institute for Biomedical Research, where his laboratory is located and all his research is conducted. He is also a professor of biology at Massachusetts Institute of Technology and Director of the MIT/Ludwig Center for Molecular Oncology.

* * *

Full Citation:

“Poised chromatin at the ZEB1 promoter enables breast cancer cell plasticity and enhances tumorigenicity”

Cell, July 3, 2013.

Christine L Chaffer (1*), Nemanja D Marjanovic (1*), Tony Lee (1), George Bell (1), Celina G Kleer (2), Ferenc Reinhardt (1), Ana C D’Alessio (1), Richard A Young (1,3), and Robert A Weinberg (1,4).

1.Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA

2. University of Michigan Medical School, Department of Pathology, Ann Arbor MI, 48109, USA

3.Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA

4.Ludwig MIT Center for Molecular Oncology, Cambridge, MA 02139, USA

*These authors contributed equally to this work.



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Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing[1]

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

Genomic instability is considered a hallmark and necessary for generating the mutations which drive tumorigenesis. Multiple studies had suggested that there may be multiple driver mutations and a plethora of passenger mutations driving a single tumor.  This diversity of mutational spectrum is even noticed in cultured tumor cells (refer to earlier post Genome-Wide Detection of Single-Nucleotide and Copy-Number Variation of a Single Human Cell).  Certainly, intratumor heterogeneity has been a concern to clinicians in determining the proper personalized therapy for a given cancer patient, and has been debated if multiple biopsies of a tumor is required to acquire a more complete picture of a tumor’s mutations.  In the New England Journal of Medicine, lead author Dr. Marco Gerlinger in the laboratory of Dr. Charles Swanton of the Cancer Research UK London Research Institute, and colleagues reported the results of a study to determine if intratumoral differences exist in the mutational spectrum of primary and metastatic renal carcinomas, pre- and post-treatment with the mTOR (mammalian target of rapamycin) inhibitor, everolimus (Afinitor®)[1].

The authors compared exome sequencing of multiregion biopsies from four patients with metastatic renal-cell carcinoma who had been enrolled in the Personalized RNA Interference to Enhance the Delivery of Individualized Cytotoxic and Targeted Therapeutics clinical trial of everolimus (E-PREDICT) before and after cytoreductive surgery.

Biopsies taken:

  • Multiregion spatial biopsy of primary tumor (representing 9 regions of the tumor)
  • Chest-wall metastases
  • Perinephric metastases
  • Germline DNA as control

Multiple platforms were used to determine aberrations as follows:

  1. Illumina Genome Analyzer IIx and Hiseq: for sequencing and mutational analysis
  2. Illumina Omni 2.5: for SNP (single nucleotide polymorphism)-array-based allelic imbalance detection for chromosomal imbalance and ploidy analysis
  3. Affymetrix Gene 1.0 Array: for mRNA analysis

A phylogenetic reconstruction of all somatic mutations occurring in primary disease and associated metastases was  performed to determine the clonal evolution of the metastatic disease given the underlying heterogeneity of the tumor.  Basically the authors wanted to know if the mutational spectra of one metastasis could be found in biopsies taken from the underlying primary tumor or if the mutational landscape of metastases had drastically changed.


Multiregion exon-capture sequencing of DNA from pretreatment biopsy samples of the primary tumor, chest wall metastases, and perinephrous metastasis revealed 128 mutations classified as follows:

  • 40 ubiquitous mutations
  • 59 mutations shared by several but not all regions
  • 29 mutations unique to specific regions
  • 31 mutations shared by most primary tumor regions
  • 28 mutations shared by most metastatic regions

The authors mapped these mutations out with respect to their location, in order to determine how the metastatic lesions evolved from the primary tumor, given the massive heterogeneity in the primary tumor.  Construction of this “phylogenetic tree” (see Merlo et. al[2]) showed that the disease evolves in a branched not linear pattern, with one branch of clones evolving into a metastatic disease while another branch of clones and mutations evolve into the primary disease.

One of the major themes of the study is shown by results that an average of 70 somatic mutations were found in a single biopsy (a little more than just half of all tumor mutations) yet only 34% of the mutations in multiregion biopsies were detected in all tumor regions.

This indicated to the authors that “a single biopsy was not representative of the mutational landscape of the entire bulk tumor”. In addition, microarray studies concluded that gene-expression signatures from a single biopsy would not be able to predict outcome.

Everolimus therapy did not change the mutational landscape.  Interestingly, allelic composition and ploidy analyses revealed an extensive intratumor heterogeneity, with ploidy heterogeneity in two of four tumors and 26 of 30 tumor samples containing divergent allelic-imbalances.  This strengthens the notion that multiple clones with diverse genomic instability exist in various regions of the tumor.

 The intratumor heterogeneity reveals a convergent tumor evolution with associated heterogeneity in target function

Genes commonly mutated in clear cell carcinoma[3, 4] (and therefore considered the prevalent driver mutations for renal cancer) include:

Only VHL mutations were found in all regions of a given tumor, however there were three distinct SETD2 mutations (frameshift, splice site, missense) which were located in different regions of the tumor.

SETD2 trimethylates histones at various lysine residues, such as lysine residue 36 (H3K36).  The trimethylation of H3K36 is found on many actively transcribed genes.  Immunohistochemistry showed trimethylated H3K36 was reduced in cancer cells but positive in most stromal cells and in SETD2 wild-type clear-cell carcinomas.

Interestingly most regions of the primary tumor, except one, contained a kinase-domain activating mutation in mTOR.  Immunohistochemistry analysis of downstream target genes of mTOR revealed that mTOR activity was enhanced in regions containing this mutation.  Therefore the intratumoral heterogeneity corresponded to therapeutic activity, leading to the impression that a single biopsy may result in inappropriate targeted therapy.   Additional downstream biomarkers of activity confirmed both the intratumoral heterogeneity of mutational spectrum as well as an intratumoral heterogeneity of therapeutic-target function.

The authors conclude that “intratumor heterogeneity can lead to underestimation of the tumor genomics landscape from single tumor biopsies and may present major challenges to personalized-medicine and biomarker development”.

In an informal interview with Dr. Swanton, he had stressed the importance of performing these multi-region biopsies and the complications that intratumoral heterogeneity would present for personalized medicine, biomarker development, and chemotherapy resistance.

Q: Your data clearly demonstrates that multiple biopsies must be done to get a more complete picture of the tumor’s mutational landscape.  In your study, what percentage of the tumor would be represented by the biopsies you had performed?

Dr. Swanton: Realistically this is a very difficult question to answer, the more biopsies we sequence, the more we find, in the near term it may be very difficult to ever formally address this in large metastatic tumours

Q:  You have very nice data which suggest that genetic intratumor heterogeneity complicates the tumor biomarker field? do you feel then that quests for prognostic biomarkers may be impossible to attain?

Dr. Swanton: Not necessarily although heterogeneity is likely to complicate matters

Identifying clonally dominant lesions may provide better drug targets

Predicting resistance events may be difficult given the potential impact of tumour sampling bias and the concern that in some tumours a single biopsy may miss a relevant subclonal mutation that may result in resistance

Q:  Were you able to establish the degree of genomic instability among the various biopsies?

Dr. Swanton:  Yes, we did this by allelic imbalance analysis and found that the metastases were more genomically unstable than the primary region from which the metastasis derived

Q: I was actually amazed that there was a heterogeneity of mTOR mutations and SETD2 after everolimus therapy?   Is it possible these clones obtained a growth advantage?

Dr. Swanton: We think so yes, otherwise we wouldn’t identify recurrent mutations in these “driver genes”

Dr. Swanton will present his results at the 2013 AACR meeting in Washington D.C. (–workshops/aacr-annual-meeting-2013.aspx)

The overall points of the article are as follows:

  • Multiple biopsies of primary tumor and metastases are required to determine the full mutational landscape of a patients tumor
  • The intratumor heterogeneity will have an impact on the personalized therapy strategy for the clinician


  • Metastases arising from primary tumor clones will have a greater genomic instability and mutational spectrum than the tumor from which it originates


  • Tumors and their metastases do NOT evolve in a linear path but have a branched evolution and would complicate biomarker development and the prognostic and resistance outlook for the patient

A great video of Dr. Swanton discussing his research can be viewed here


Everolimus: an inhibitor of mTOR

The following information was taken from the New Medicine Oncology Database (




Approved/Filed Indications

Novartis PharmaCurrent as of: August 30, 2012 Generic Name: Everolimus
Brand Name: Afinitor
Other Designation: RAD001, RAD001C
RAD001, an ester of the macrocytic immunosuppressive agent sirolimus (rapamycin), is an inhibitor of mammalian target of rapamycin (mTOR) kinase.Administration Route: intravenous (IV) • PO • solid organ transplant
• renal cell carcinoma (RCC), metastatic after failure of treatment with sunitinib, sorafenib, or sunitinib plus sorafenib
• renal cell carcinoma, advanced, refractory to treatment with vascular endothelial growth factor (VEGF)-targeted therapy
• treatment of progressive neuroendocrine tumors (NET) of pancreatic origin (PNET) in patients with inoperable, locally advanced or metastatic disease

Marker Designation
Gene Location

Marker Description


5’-AMP-activated Protein Kinase (AMPK)AMPK beta 1 (beta1 non-catalytic subunit) • HAMPKb (beta1 non-catalytic subunit) • MGC17785 (beta1 non-catalytic subunit) • AMPK2 (alpha1 catalytic subunit) • PRKAA (alpha1 catalytic subunit) • AMPK alpha 1 (alpha1 catalytic subunit) • AMPKa1 ( AMPK is a member of a metabolite-sensing protein kinase family found in all eukaryotes. It functions as a cellular fuel sensor and its activation strongly suppresses cell proliferation in non-malignant cells and cancer cells. AMPK regulates the cell cycle by upregulating the p53-p21 axis and modulating the TSC2-mTOR (mammalian target of rapamycin) pathway. The AMPK signaling network contains a number of tumor suppressor genes including LKB1, p53, TSC1 and TSC2, and modulates growth factor signaling involving proto-oncogenes including PI3K, Akt and ERK. AMPK activation is therefore therapeutic target for cancer (Motoshima H, etal, J Physiol, 1 Jul 2006; 574(Pt 1): 63–71).AMPK is a protein serine/threonine kinase consisting of a heterotrimeric complex of a catalytic alpha subunit and regulatory ß and gamma subunits. AMPK is activated by increased AMP/ATP ratio, under conditions such as glucose deprivation, hypoxia, ischemia and heat shock. It is also activated by several hormones and cytokines. AMPK inhibits ATP-consuming cellular events, protein synthesis, de novo fatty acid synthesis, and generation of mevalonate and the downstream products in the cholesterol synthesis pathway (Motoshima H, etal, J Physiol, 1 Jul 2006; 574(Pt 1): 63–71). – ovarian cancer
– brain cancer
– liver cancer
– leukemia
– colon cancer
CREB regulated transcription coactivator 2 (CRTC2)TOR complex 2 (TORC2, mTORC2) • RP11-422P24.6 • transducer of regulated cAMP response element-binding protein (CREB)2 • transducer of CREB protein 2 • TOR1Location: 1q21.3 The mammalian target of rapamycin (mTOR) exists in two complexes, TORC1 and TORC2, which are differentially sensitive to rapamycin. cAMP response element-binding protein (CREB) regulated transcription coactivator 2 (CRTC2) or TORC2 is a multimeric kinase composed of mTOR, mLST8, mSin1, and rictor. The complex is insensitive to acute rapamycin exposure and functions in controlling cell growth and actin cytoskeletal assembly.TORC2 controls gene silencing, telomere length maintenance, and survival under DNA-damaging conditions. It is primaily located in the cytoplasm but also shuttles into the nucleus (Schonbrun M, etal, Mol Cell Biol, Aug 2009;29(16):4584-94). – brain cancer
Hypoxia inducible factor 1 alpha (HIF1A)HIF1-alpha (HIF-1 alpha) • HIF-1A • PASD8 • MOP1 • bHLHe78Location: 14q21-q24 The alpha subunit of the hypoxia inducible factor 1 (HIF-1alpha) is a 826 amino acid antigen consisting of a basic helix-loop-helix (bHLH)-PAS domain at its N-terminus. HIF-1alpha is rapidly degraded by the proteasome under normal conditions, but is stabilized by hypoxia resulting in the transactivation of several proangiogenic genes. HIF-1alpha is responsible for inducing production of new blood vessels as needed when tumors outgrow existing blood supplies. HIF-1alpha serves as a transcriptional factor that regulates gene expression involved in response to hypoxia and promotes angiogenesis.HIF-1alpha is a proangiogenic transcription factor induced primarily by tumor hypoxia that is critically involved in tumor progression, metastasis and overall tumor survival. HIF-1alpha functions as a survival factor that is required for tumorigenesis in many types of malignancies, and is expressed in a majority of metastases and late-stage tumors. HIF-1alpha is overexpressed in brain, breast, colon, endometrial, head and neck, lung, ovarian, and pancreatic cancer, and is associated with increased microvessel density and/or VEGF expression – prostate cancer
– bladder cancer
– nasopharyngeal cancer
– head and neck cancer
– kidney cancer
– pancreatic cancer
– endometrial cancer
– breast cancer
Mammalian target of rapamycin (mTOR)FK506 binding protein 12-rapamycin associated protein 1 • RAFT1 • FK506 binding protein 12-rapamycin associated protein 2 • FRAP • FRAP1 • FRAP2 • RAPT1 • FKBP-rapamycin associated protein • FKBP12-rapamycin complex-associated protein 1 • rapamycin target protein • TOR • FLJ44809 • MTORC1 • MTORC2 • RPTOR • RAPTOR • KIAA1303 • mammalian target of rapamycin complex 1Location: 1p36.22 The mammalian target of rapamycin (mTOR) is a large serine/threonine protein (Mr 300,000) having heat repeats, and protein-protein interaction domains at its amino terminus, and a protein kinase domain at its carboxy terminus. mTOR is a member of the phosphoinositide 3-kinase (PI3K)-related kinase (PIKK) family and a central modulator of cell growth. It regulates cell growth, proliferation and survival by impacting on protein synthesis and transcription. mTOR is present in two multi-protein complexes, a rapamycin-sensitive complex, TOR complex 1 (TORC1), defined by the presence of Raptor and a rapamycin insensitive complex, TOR complex 2 (TORC2), with Rictor, Protor and Sin1. Rapamycin selectively inhibits mTORC1 by binding indirectly to the mTOR/Raptor complex via FKBP12, resulting in inhibition of p70S6kinase but not the mTORC2 substrate AKTSer473. Selective inhibition of p70S6K attenuates negative feedback loops to IRS1 and TORC2 resulting in an increase in pAKT which may limit the activity of rapamycin.In a hypoxic environment the increase in mass of solid tumors is dependent on the recruitment of mitogens and nutrients. As a function of nutrient levels, particularly essential amino acids, mTOR acts as a checkpoint for ribosome biogenesis and cell growth. Ribosome biogenesis has long been recognized in the clinics as a predictor of cancer progression; increase in size and number of nucleoli is known to be associated with the most aggressive tumors and a poor prognosis. In bacteria, ribosome biogenesis is independently regulated by amino acids and energy charge. The mTOR pathway is controlled by intracellular ATP levels, independent of amino acids, and mTOR itself is an ATP sensor (Kozma SC, etal, AACR02, Abs. 5628). – breast cancer
– pancreatic cancer
– multiple myeloma
– liver cancer
– brain cancer
– prostate cancer
– kidney cancer
– lymphoma
Signal transducer and activator of transcription 3 (STAT3)Stat-3 • acute-phase response factor (APRF) • FLJ20882 • HIESLocation: 17q21 Signal transducer and activator of transcription 3 (STAT3) is a member of the STAT protein family. STAT3, plays a critical role in hematopoiesis. STAT3 is located in the cytoplasm and translocated to the nucleus after tyrosine phosphorylation. In response to cytokines and growth and other activation factors, STAT family members are phosphorylated by the receptor associated kinases and then form homo- or heterodimers, which translocate to the cell nucleus where they act as transcription activators. – multiple myeloma
– hematologic malignancy
– lymphoma
Sonic hedgehog homolog (SHH)Shh • HHG1 • HHG-1 • holoprosencephaly 3 (HPE3) • HLP3 • SMMCILocation: 7q36 Sonic hedgehog, a secreted hedgehog ligand, is a human homolog of the Drosophila segment polarity gene hedgehog, cloned by investigators at Harvard University (Marigo V, etal, Genomics, 1 Jul 1995;28 (1):44-51).The mammalian sonic hedgehog (Shh) pathway controls proliferation of granule cell precursors in the cerebellum and is essential for normal embryonic development. Shh signaling is disrupted in a variety of malignancies. – pancreatic cancer
– CNS cancer


1.         Gerlinger M, Rowan AJ, Horswell S, Larkin J, Endesfelder D, Gronroos E, Martinez P, Matthews N, Stewart A, Tarpey P et al: Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. The New England journal of medicine 2012, 366(10):883-892.

2.         Merlo LM, Pepper JW, Reid BJ, Maley CC: Cancer as an evolutionary and ecological process. Nature reviews Cancer 2006, 6(12):924-935.

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