Cancer Biomarkers

Cancer Biomarkers

  • Sandeep Telkar added an answer:
    How to construct TGF-β induced EMT( Epithelial to mesenchymal transition) pathway?

    In my work am trying to construction EMT( Epithelial to mesenchymal transition) pathway induced by TGF-β but I am finding difficulties while construction i.e.,
    whether pathway constructed for particular cancer is effective or in general
    (because the TGF-β downstream signals are same i e SMAD and non-SMAD signal are same for all type of cancer)

    Sandeep Telkar

    thank you  Shyam Nyati  for your suggestions construction means Construction of the protein interaction network. I am trying to construct protein interaction network that induced by TGF-b during the event EMT.

  • Horatiu Cristian Popescu added an answer:
    Why mutant p53 expression is increased in colorectal adenocarcinoma obese- type2 diabetes mellitus patients?

    Is there a particular feature or a direct connection that can explain why immunohistochemical expression of mutant protein p53 is increased in obese and diabetics (type 2 diabetic) patients at diagnosis of colorectal adenocarcinoma compared to non -obese diabetics versus non-diabetics obese/non obese?

    Study included immunohistochemical analysis of  2 proteins Bcl2 and p53 (both monoexpression and coexpression) in 100 newly  diagnosed colorectal adenocarcinoma specimens divided  equal in 2 groups diabetics (type 2 diabetes mellitus already existing at diagnosis of colorectal cancer)  and non-diabetics .The preliminary statistics results have not indicated a significant difference between the 2 groups, in terms of Bcl2, but  indicates an increased expression of p53 only in the  diabetic-obese group compared to  non-diabetics obese or non-obese (statistically significant ) which theoretically indicates a contact point between obesity, cancer and diabetes. Interestingly moderately low degree of differentiation is associated with both diabetes and the presence of p53 positivity; G2-p53 associations is an intriguing part. Bcl2 expression was low and insignificant in both group.

    Horatiu Cristian Popescu

    Thank you for your clear and concise information you gave me that will help me a lot. Best, Horatiu

  • Robert Kiss added an answer:
    Most of the biomarkers of GBM based on proteins are common to other cancer also (EGFR,VGEF,PTEN,MGMT etc). How can it be specific for glioma?
    What is the most specific marker of glioblastoma. Where this biomarker science leaning toward?
    Robert Kiss

    I fully agrees with Reza's responses / comments.

    You must clearly "subdivide" the terms biomarkers in:

    • diagnosis (GFAP is a specific marker of astroglioma, but can also be overexpressed in reactive astrocytes)
    • prognosis
    • treatment responses,
    • etc..

    the attached articles could may be of help for you.

    Best regards


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  • Héctor Osorio-Vega added an answer:
    At this moment, are there any specific markers to detect the presence of cancer stem cells or cancer dormant cells in soft tissue?

    The event of death by metastasis or recurrence is very common, many researchers have linked the tendency of some tumors to re-appear to the presence of occult or dormant cancer cells that may have a phenotype that allows them to remain "hidden" from the immune response. However, the understanding of these cells and the mechanisms that they use to achieve evasion remain mostly unknown. It is critical to understand these cells better and to be able to detect their presence for they are of great therapeutic importance.

    Héctor Osorio-Vega

    currently my interest is in Colorectal cancer, this one have a very predictable behaviour, however, i haven't been able to find any specific marker. The best option is to target the overxpression of MMP-7 and/or beta Catenin, but i would expect them to not be so present in residual cells that are dormant, or in cancer stem cells that have a very slow metabolism.

  • Giovanni Colonna added an answer:
    Cancer a mere matter of luck? Or is there something under-appreciated?

    It has been all over in the news lately: The majority of cancer is obtained by bad luck, not by lifestyle or inheritance. See attached. 

    Really? The data appear solid and they make sense, but the conclusion seems a bit premature: the observations are based on established risk factors in the USA and I assume (let the experts please come forward!) that these risk factors are based on occurrence. This means we do not see all those cases where the patient's immune system adequately takes care of the anomaly. 

    How does occurrence of cancer relate to failure of the patient's immune system, and can we monitor this based on adequate biomarkers? How will the statistics and the conclusions change when this factor is included in the analysis?

    Giovanni Colonna

    As I said, luck does not exist. It's the man who by his intelligence is preparing to jump on the bandwagon of the fortune, when it passes. This is what is said where I come from, in a city that has at least three thousand years of history (Naples, Italy). The luck is the result of human actions, poor human actions produce unmanageable facts or unclear, then we say it is the fault of bad luck. In cancer we proceed inadequately and this allows everyone to discuss everything and the opposite of everything. We know only the macroscopic aspects of the molecular biology of the cell, almost nothing of the cancer biology and nonetheless we expect to discover drugs that can cure cancer. The answer is in the facts. However, the real question is: what’s wrong? What is the human action, scientific, or socio-political, or socio-cultural, or methodological that is wrong? Only by answering these questions, we will be able to find the right way. I don't want to be lacking in respect towards someone, but any other argument is unnecessary debate, already heard for decades.

  • Alejandro Martin added an answer:
    Clone having repetitive sequence insert and its discripancy upon scale up?

    I have cloned my 3.3Kb insert having repetitive sequence in yeast expression vector, by directional cloning in E.coli. Positive Clone of 8.7Kb was confirmed by restriction analysis. While the same positive E.coli transformants when grown in 100ml LB, the restriction pattern observed is different. But the the digestion pattern is as expected when it is isolated from 5ml culture. Could anyone please let me know why this discrepancy observed from 5ml to 100ml scale up.

    Alejandro Martin

    The more doublings of your population, the higher the probability that mutants bearing deletions will arise and overtake the culture. Most likely you already have mutants in the 5 mL culture, but at proportions low enough to pass below the limit of detection of your assay (restriction digestion + gel electrophoresis).

    Have you tried E. coli strains designed to propagate repetitive sequences, such as SURE or STBL3?

  • Massoud Vosough added an answer:
    What is marker of malignant transformation in cultured cells?

    I am planning to culture MCF10 cells with different carcinogens,can some suggest a marker which I can look for as a sign of early malignant transformation.


    Massoud Vosough

    The epithelial-mesenchymal transition (EMT) is a process in which epithelial cells lose their cell polarity and cell-cell adhesion, and gain migratory and invasive properties to become mesenchymal stem cells. E-cadherin is a protein that in humans is encoded by the CDH1 gene and down regulated during early stages of carcinogenics.

    Good Luck

  • Volker Gatterdam added an answer:
    Where we can order cancer aptamers?

    Sensing with the help of aptamers.

    Volker Gatterdam

    Dear Narayanaswamy,

    maybe you can also find interesting "aptamers" at SOMAlogic ( They are selling small binders, which are a hybride between DNA and Protein.

    Regards Volker

  • Stephane Chartier added an answer:
    What should be positive control for IHC and western blotting during experiments to prove whether an untested protein could be a biomarker for cancer?

    I'm going to design a study to test whether an untested protein could be a biomarker for pacreatic cancer.  I intend to do immunohistochemistry of the pancreatectomy tissue of the patients with pancreatic cancer, benign  tumour and disease - free.  I will also do Western blotting and ELISA.  Could you please suggest me in terms of positive control selection for these tests?

    Stephane Chartier

    Hi Saif! I'm not too familiar with Westerns and ELISA but I have done extensive IHC work on muscle and skeletal tissue in mouse cancer models. Typically you'd check the data sheet on any given Ab to see what positive controls the manufacturer recommends. Given that your Ab is untested, I would simultaneously stain for an Ab which will be widely expressed in any tumor alongside your untested Ab. I would recommend CD68, a marker of the myeloid lineage and macrophages. Also, CD31, a marker of endothelial cells is expressed robustly in tumors. Hope this helps!

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  • Vladimir S Kurćubić added an answer:
    Do you know what is the level of MMP-9 in the breast cancer tissue?

    Hello everyone,

    Do you know what is the level of MMP-9 in the breast cancer tissue?

    Vladimir S Kurćubić

    Draga Danijela, 

    Nema na čemu. 


  • Saif U. Sikdar added an answer:
    Is it possible to validate an untested protein as a biomarker for pancreatic cancer solely by immunohistochemistry?

    I want to design a study to assess whether an untested protein could be used as a biomarker for human pancreatic cancer.  I intend to do immunohistochemistry of this protein in pancreatic tumour tissue and normal tissue.  I am thinking of doing TMA and normal tissue microarray. Should I include any other assays like ELISA of body fluids and Western blotting for validating this protein?

    Saif U. Sikdar

    I have also found people doing MALDI-TOF and MS.  Which test will be more practical for clinical diagnosis?

  • Graham Dellaire added an answer:
    What are the main biomarkers/ molecules to study in HNSCC in DNA damage pathway because of radiotherapy?

    We are following HR and NHEJ pathway. Want to know the assays and techniques to go ahead

    Graham Dellaire

    Re: 8-OXOdG ... Not sure how useful (or appropriate) detection of 8-OXOdG is going to be for general surveillance of DNA double-strand break (DSB) repair by HR and NHEJ.

    8-OXOdG is a measure of base-excision damage and the BER pathway has nothing to do with NHEJ or HR, which are DNA double-strand break repair pathways.  For general DSB repair competence, good old phospho-S139 H2A.X (i.e. gamma-H2A.X) is the gold standard for most IR dose experiments especially in vitro.  If you cells are cycling, BRCA1 or RAD51 foci formation are good markers of HR ability. Otherwise you need to do reporter assays for NHEJ and HR specifically.

    We developed one such assay for HR, that relies on CRISPR-mediate homology directed repair, see: Pinder et al., 2015 NAR

    Cheap, quick, fast.


    Doc Dellaire

  • Govind Babu K added an answer:
    I am creating a roadmap for high risk wilms tumor for a research institute. Does anyone have a cell line data for high risk wilms?

    These cell lines along with available xenografts and other factors along with other biomarkers ( if you have any it would be appreciated)  will be used to build a preclinical model for high risk Wilms tumors.  The development of assays specific to this model will result in the ability to do novel cell line and animal testing which could potentially lead to clinical trials with new compounds for children with these disease.

    Govind Babu K

    sorry no

  • Yaser Arjeyni added an answer:
    What are the transcript variants for BRCA1 and where can I find the BRCA1 exons?

    I know BRCA1 on ch17q21 have 29 transcript variants I found 7 of them on NCBI but, I couldn't find others.
    Can anyone please help me find them?
    Also I know BRCA1 has 24 exons, but where can I find their range on DNA?

    I would appreciate any help.

    Yaser Arjeyni


    You have not specified aim of your study but overall i think the variants you have found on NCBI must be responsive for your survey.

  • David S Guttery added an answer:
    Is it possible to use CAST PCR technology for cell free DNA analysis?
    I am trying to find out the most "sensitive" methods for detection of specific DNA mutation in serum/plasma samples. Does anybody have any knowledge on the issue?
  • Samah Oda added an answer:
    What is the role of LC50/LD50 value of any compound or metal for toxicological or other studies?
    Why do we calculate only LC50? Why not 30, 40 or other values?
    Samah Oda

    How could I calculate the acute toxic dose from LD50? Is LD50 is acut dose

  • Luboshits Galia added an answer:
    How can I find the complete profile of specific marker production by individual cells?

    For example what proteins and receptors are produced in normal breast cells and malignant cells.

    Luboshits Galia

    you can run protein antibody array and compare the expression in normal versus malignant tissue

  • Lin-Lin Bu added an answer:
    NF-kB and JAK/STAT3 pathways crosstalk, (IL-6??)?

    Hello everyone.

    I am looking at studying the connection between NF-kB and JAK/STAT3 in normal and cancer cells. I am pretty certain from my research that there is a connection with IL-6. What type of tests should I propose to test this and what would some expected results be?

    Thank you!

    Connor Hoge

    Lin-Lin Bu

    “NF-κB and STAT3 – key players in liver inflammation and cancer” maybe this review could have some help for you.

  • Ishtiaq Qadri added an answer:
    Can we use any other cell surface marker in addition to CD33, CD133, CD24, CD44, CD90 DLK1, EpCAM, Ov6 for hCSC Isolation from HCV HCC biopsies?

    HCC, hepatic Cancer Stem Cells, HCV GT4, intratumoral heterogeneity, FACS

    Ishtiaq Qadri

    Dr Khedar: Thank you for your referral. My question is related to liver and hepatic cancer stem cells and it seems that Dr Ahamd;s expertise is on estrogen receptors and  p53 in the context of prostate and breast cancer. 

  • Abdul Hafeez Kandhro added an answer:
    Do low glucose conditions stabilise HIF1 alpha protein in Breast Cancer Cell lines?

    Do low glucose conditions stabilise HIF1 alpha protein in Breast Cancer Cell lines? Specifically in high glycolytic cells like MDA-MB series.

    Abdul Hafeez Kandhro

    Under normal oxygen conditions, nonmetastatic cells consume less glucose and express low HIF-1α, whereas metastatic cells constitutively express high glycolysis and HIF-1α, suggesting that dysregulation of HIF-1α may induce the Warburg effect.

    The recent discovery and study of HIF-1α have implicated a possible molecular mechanism for the Warburg effect in malignant tumors. HIF-1α plays an important role in cellular responses to hypoxia and other stresses. HIF-1α combines with HIF-1β to form a heterodimeric transcription factor that regulates the expression of glycolytic and angiogenic proteins. HIF-1α is constitutively expressed and destabilized in the presence of O2 by proline hydroxylation and is targeted for proteosomal degradation by the von Hippel-Lindau (vH-L) ubiquitin ligase. When accumulated (e.g., under hypoxia), the HIF-1 complex binds hypoxia response elements (HREs; canonically CCATG) in the promoter region of target genes.

    To know  the relationship between HIF-1α stabilization in oxygenated conditions and the Warburg effect; by comparing glucose transport, lactate production, HIF-1α protein, and HRE-induced transcript levels in metastatic (MDA-mb-435) and nonmetastatic (MCF-7) breast cancer lines. Under a 20% oxygen atmosphere (normoxia), MDA-mb-435 cells have elevated glycolysis, HIF-1α, and HRE transcripts, whereas these parameters are measurably lower in MCF-7 cells. Hypoxia (≤2% oxygen) induced no change in the glycolytic phenotype in MDA-mb-435 cells, whereas HIF-1α, HRE transcripts, and glycolysis were profoundly induced in MCF-7 cells. But due to controversial findings have identified MDA-mb-435 cells with melanoma cells due to the expression of specific melanocyte genes and lack of expression of breast cell line genes in MDA-mb-435 sublines. To account for this possible discrepancy, renal cell carcinoma (RCC4) used, where transfection of the vH-L gene into a vH-L-null line directly modulated HIF-1α levels. Parental RCC4 cells functioned similarly to the MDA-mb-435 and MDA-mb-231 lines by expressing high levels of HIF-1α and exhibiting high glycolysis under normoxic conditions. There was a minimal effect when these cells were switched to hypoxia. Restoration of vH-L activity led to normalization of the HIF-1α response. Under normoxia, RCC4/vH-L cells demonstrated low rates of glycolysis, which subsequently increased in hypoxia. 

    You may find details in this article: "Hypoxia-Inducible Factor-1α and the Glycolytic Phenotype in Tumors"

  • Udesh Dhawan added an answer:
    How do you recognise epithelial-to-mesenchymal transformed (EMT) cancer cells in clinical samples?
    They should have reduced or absent epithelial characteristics, so how do you discriminate them from authentic mesenchymal cells?
    Udesh Dhawan

    Dear Dr. Ericsson, I have been working with something similar and I have found decreased CDH1 to be a good reference for the loss of Epithelial Characteristics and an increase in CDH2, Vimentin plus a spindle shaped morphology to know that the cells have mesenchymal characteristics. Moreover, I have also found the expression of Snail and Slug to be highly increased in the cells showing the mesenchymal characteristics since they control CDH1 gene. But in all of my experiments, I have found Twist to be downregulated. So, I would suggest that a decrease in CHD1, Increase in CHD2, Vimentin and an increase in any of these transcription factors (Snail, Slug and/or Twist) followed by an elongated/spindle morphology should be a good observation to conclude that your cancer cells have transitioned from Epithelial to Mesenchymal state.

  • Carol A Gray added an answer:
    Is there a well-established research protocol to induce prostate cancer in dogs and are there good biomarkers?

    I am part of a multidisciplinary research group at the University of Saskatchewan Canada, who are studying prostate cancer. I am wondering if there is well established research protocol to induce prostate carcinoma in dogs. We need dogs with prostate carcinoma to use for imaging studies.

    Anybody who has a protocol or can help do this and would like to establish collaboration?

    Thanks very much

    Ahmad Al-Dissi                                                                            

    Carol A Gray

    Agree with the answers above; ethically, most researchers now think that companion animals (cats and dogs) must benefit from any cancer research that involves using them, so naturally occurring cases are the only option.

  • Stefania Zuppone added an answer:
    Does anyone know about a Her2+ breast cancer cell line over-expressing uPAR?

    Hi everyone!

    I'm searching for a breast cancer cell line in which Her2 and uPAR are both over-expressed. Does anyone know about any? Thanks in advance

    Stefania Zuppone

    Thank you so much for your help and kindness!

  • Hatem A Abou-Ouf added an answer:
    Any advice on prostate Cancer cell lines, genome portal?

    Hi, I am looking for a source to get copy number data for prostate cancer cell lines such as PC3, LNCaP, DU145 , ..etc. 

    I checked Oncomine but i can not find these data. Share plz if you have a clue. 


    Hatem A Abou-Ouf

    Thanks Michele. However, i am looking for a data base that i can search/query. 

  • Fawaz Naji Saleh Al-Shaheri added an answer:
    How can I identify and evaluate patients who are at high risk to get leukemia?

    How I can evaluate patients whom at high risk to get leukemia, , I'm asking about lab technique by which I can expect if patients at risk to be leukemic?

    Fawaz Naji Saleh Al-Shaheri

    You are welcome and best of luck.

  • Piero Tosi added an answer:
    Can all malignant tumors (cancers) metastasize to other organs?
    Cancers metastasize via seeding through blood or lymphatic vessels.
    Piero Tosi

    I agree with Jarad and Momma, with the exception for glioblastomas in very rare cases.

  • Mehrdad Payandeh added an answer:
    What is the new tumor suppressor gene for prostate cancer?

    For evaluation of tumor response and toxicity in prostate cancer cells.

    If we want to check the cancer cells response to the adjuvant radiation therapy or combination of three or two modalities in prostate cancer, what biomarker could help us? What is the newer and recent androgen receptor?

    Mehrdad Payandeh

    Ki67 level and mitotic index

  • Steve Mcclellan added an answer:
    What stemness genes can be used for cell classification using expression data?

    I have sequenced tens of single cells of bladder cancer, and got the gene expression profile of each single cell. I am trying to speculate the cancer stem cells mixed in these cells using clustering method, which needs a priori list of "stemness genes". If there are some available common or specific stemness signatures can be used in this analysis? Many thanks.

    Steve Mcclellan

    The ES markers Nanog, Sox2 and Klf4 are relevant to CSC and can be used to differentiate stem versus non-stem cancer cells.  Please see our most recent paper using SmartFlare to detect CSC (you can download it in my profile).  Other relevant markers are players in the Wnt, notch or sonic hedgehog pathways as these are unregulated in most CSC.  Other surface markers are CXCR4 (Cd184) and MDR1 (CD243) and Muc1 (CD227).

    Kind regards,


  • Tahmina C Islam added an answer:
    Can cancer come from any type of cell or are there some cell types that never produce cancer?
    Some cells seem to produce cancers more frequently than others. There are > 200 distinct human cell types; do all of these produce cancers under some circumstances? If not what is special about cells that never produce cancer? Why do some cells produce cancer relatively frequently while others do not? How well is this predisposition toward or against cancer development understood?
    Tahmina C Islam

    Wonderful discussion and a very nice question,Just adding some points to the discussion. With the development in high throughput techniques and specific molecular, biological, clinical research coming together, many aspects of cancer initiation-formation, biology, progression are unravelling such as cell type specificity, stem cell origin of cancer, transcriptions factors for pluripotency vs differentiation, genetic errors and mutations, epigentic and immunological factors along with socioeconomic factors, ethnicity, and geographical location (diet) regarding the incidence and understanding of cancer.

    I think the cells that are most prone to cancers depends on their exposure to the hits involved in cancers and also their proliferative and differentiation status.
    1. So epithelial cancers are the commonest such breast, prostate, lung, colorectal.
    2. then Melanoma, Lymphoma, Leukemia, the list varies with the location in the globe, ofcourse.
    3. Neuoblastomas is a rare cancer that occurs in the children, while most brain tumours develop from cells that support the nerve cells.
    4. And many rare tumours that are found in the 'rare list' are very specific such as Merkel cell skin cancer, Angiosarcoma of the heart. Very well differentiated cell types are may be not switched back to pluripotency easily or may be these cell types not easily exposed to triggering mechanisms as are the cancer stem cells.
    I would like to bear in mind the basic cell types and the location of their stem cell type in our body keeping in mind their normal functionality and derailment from it, by DNA damage and also their normal proliferative and apoptotic signals (as the damaged cells are may not be cleared) regulates how common or how rare a tumour may be. Ofcourse other factors mentioned above do come into play.

    How a stem cell becomes a cancer stem cell having the multipotent capacity by acquiring genetic modifications is vital, as clonaity of cancer has shown that origin of the tumour goes back to a primary cancer stem cell. It is important to be hit by one or multiple mutations by triggering agents in the environment (bacterial, viral or toxic) and the cells proliferative capacity allowing it not to be able to repair the damage or other enzymes or molecules in the repair pathways being ineffective. Also, epigenatic mechanisms may come into play along with the genetic aberrations in the mutihit process of cancer formation and progression.

    The refs below in cancer biology, progression and pluripotency factors may help further understanding.
    2.Cell. 2006 Aug 25;126(4):663-76. Epub 2006 Aug 10.
    Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors.
    Takahashi K1, Yamanaka S.

About Cancer Biomarkers

A biological molecule found in blood, other body fluids, or tissues that is a sign of a normal or abnormal process, or of a condition or disease. A biomarker may be used to see how well the body responds to a treatment for a disease or condition. Also called molecular marker and signature molecule. A cancer biomarker pertains to any biomarker that fits the aforementioned definition but only for cancer, and no other disease.

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