Cancer Biomarkers

Cancer Biomarkers

  • Ademola Popoola added an answer:
    Does anyone want to collaborate on optical studies of prostate cancer and the use of gold nanoparticles as contrast agents for detection of PC?
    I’d like to set up collaboration with those who have an access to human and/or canine prostates with cancer and might be interested in 1) exploring interstitial optical studies of prostates with cancer for diagnostic purposes and 2) using gold nanoparticles as contrast agents for prostate cancer detection. The goal is two-fold. First, we want to establish a correlation between concentrations of major chromophores like Hb, HbO2 and H2O and a presence of PC, as well as measure optical absorption and scattering parameters of the organ on ex vivo excised prostates. Since those prostates will be excised anyway we’d like to perform optical measurements on them after excision before they go for some other destructive tests etc. Once this stage is completed and data make sense, we can proceed to a development of an endoscope for performing such measurements in vivo (illumination via rectum, detection via urethra). The approach would be similar to cystoscopy and will utilize a side-firing fiber (or its variation) as a detector and a cylindrical diffuser as the light source. Second, we would like to target PC biomarkers (like PSMA) in the gland, functionalize gold nanoparticles with appropriate surface agents, deliver Au NPs to the prostate with cancer and detect them with the same technique (illumination via rectum, detection via urethra). This project is more challenging on a number of reasons: 1) preparing Au NPs for targeting PMSA and still protected from RES that can be efficiently accumulated in the gland has never been done (most studies in vitro); 2) since such studies would require working with Au NPs and patients, FDA approval can be an issue. Doing these experiments in dogs would be almost ideal. However, there are conflicting reports on PSMA as a biomarker in canine prostate cancer (see below). Thus, if PSMA can indeed be used and targeted in canine PC, no human prostates would be involved and entire experiments can be performed on canine prostates. https://www.researchgate.net/post/Expression_of_PSMA_in_human_vs_canine_prostate_a_useful_biomarker_in_PC_studies_in_the_canine_model_or_NOT Why not going with rats, for example? Because of the size of the prostate. We really want to go through cm’s of prostate tissue, and dog’s prostate is almost an ideal substitute for a human prostate (sizewise). On the other hand, we’d like to target realistic Au NPs concentrations in the prostate that can be achieved in such studies. So, I’d really like to get your thoughts and possibly practical suggestions on this aspect. I do believe that such molecular imaging of PC via optical detection of Au NPs may not only improve the early cancer detection but pave the way for Au NPs-mediated thermal therapies for focal cancer ablation (but this is a scientist talking:) The nature of this project would require a multidisciplinary team of oncology urologists, molecular biologists, chemists. We can detect Au NPs in the prostate via urethra using optical radiance technique. Moreover, the sensitivity is much better than the sensitivity of the clinical CT (see the comparison in the publication and relevant references). We can see <=10^10 Au nanorods in the prostate. It means that with saturating of 1-10% of existing PSMA copies per cell ( close to 10^6 sites per cell), detecting 10^10 Au NPs would correspond to seeing ~10^5 malignant cells in the prostate. This number corresponds to the so-called angiogenic switch indicating very promising potential for early cancer detection. More details on the method are provided in our recent publication (below). I encourage you to read it, and I’d be happy to discuss logistics and answer questions on this topic because there is no way to address all relevant issues in this posting. Really looking forward for the feedback! https://www.researchgate.net/publication/262003897_Feasibility_of_interstitial_near-infrared_radiance_spectroscopy_platform_for_ex_vivo_canine_prostate_studies_optical_properties_extraction_hemoglobin_and_water_concentration_and_gold_nanoparticles_detection?ev=prf_pub
    Ademola Popoola · University of Ilorin
    This is quite good and has great prospect in the future of the management of prostate cancer. I work in a big tertiary center in Nigeria with a catchment population of about 10 million and increasing number of patients with prostate cancer. We will be glad to be involved in collaboration My email : Ademola67@yahoo.com, ademolapopoola@unilorin.edu.ng
  • Qilong Wang added an answer:
    Can anybody tell us which antibody (For IHC) works best in liver cancer induced rats?
    Hepatocarcinogenesis.
    Qilong Wang · James Brown Cancer Center
    i always use LifeSpan BioScience, Inc. 's antibodies for IHC, i think it is best one
  • Karnika Singh added an answer:
    DNA fragmentation protocol - can anyone help?
    Without using kit.
    Karnika Singh · Louisiana State University Health Sciences Center Shreveport
    Which protocol did you use for DNA fragmentation analysis?
  • Saurabh Chauhan added an answer:
    Why does probe lifetime change when bound to cancer cells?
    Could the small change in lifetime arise from additional multiple scattering of fluorescence/excitation photons by large volume of tumor? I also wonder if anyone could estimate refractive index of cancer tissue and compare it to normal. Probes change lifetimes as much as 10% when refractive index of its media changes by about the same.
    Saurabh Chauhan · University at Buffalo, The State University of New York
    I am very new to this field, but If I would have to guess, fluorescence anisotropy could potentially affect the lifetimes. If you attach a big molecule to your fluorophore, its rotational correlation time changes and the emitted light remains polarized for a longer time. For ruling out scattering, you could use a longpass filter in the emission path which would stop the scattering photons from the sample. Saurabh
  • Faizan Shukor added an answer:
    Do you think biomarkers are the future of medicine?
    Http://acceleratingscience.com/proteomics/strategy-for-cancer-biomarker-verification-using-srmmrm-mass-spectrometry/
    Faizan Shukor · National University of Malaysia
    Predicting a disease is a very challenging work because absolute values of risk factors sometimes correlate poorly with asymtomatic individuals. I believe biomarkers can be utilize in the future in targeting prevention strategies appropriately.
  • Esraa Tamim added an answer:
    What are the methods of fixation and processing that are most suitable for liver cancer cells/colon carcinoma?
    Are the same processing and fixation methods applicable to all cancers?
    Esraa Tamim · Egyptian Atomic Energy Authority
    colon tissue was rapidly dissected and excised, rinsed in saline solution and cut into suitable pieces, then fixed in neutral buffered formalin (10%) for 24 hours, following fixation, the specimens were dehydrated in ascending series of alcohol, then tissue specimens were cleared in xylene and embedded in paraffin at 60 ºC. Section of 5 microns thickness was cut by slidge microtome. The obtained tissue sections were collected on the glass slides and stained by haematoxylin and eosin stain for histopathological examination by the light microscope. for IHC Colon tissue samples were fixed in 10% phosphate-buffered formalin for 10 h at 4°C, dehydrated in ascending concentrations of ethanol, cleared with xylene, and embedded in PolyFin (Triangle BiomedicSciences).
  • Expression of PSMA in human vs. canine prostate: a useful biomarker in PC studies in the canine model or NOT?
    I've found two groups of articles that state different conclusions. According to Aggarwal S, Ricklis RM, Williams SA, Denmeade SR, "Comparative study of PSMA expression in the prostate of mouse, dog, monkey, and human," (Prostate. 2006 Jun 15;66(9):903-10), "PSMA is not expressed in any significant amount in the prostates of mouse, beagle dog, or macaque monkeys in this study but is expressed in high levels by human prostate. These non-human species, therefore, are not suitable toxicologic models to assess prostate damage from PSMA-activated intraprostatic prodrug/protoxin therapies." However, in the more recent article of Schmidt S, Fracasso G, Colombatti M, Naim HY, "Cloning and characterization of canine prostate-specific membrane antigen," (Prostate. 2013 May;73(6):642-50) it's stated that "We demonstrate that canine PSMA reveals similar characteristics to human PSMA rendering this protein useful as a translational model for investigations of prostate cancer as well as a suitable antigen for targeted therapy studies in dogs." Another recent article below appears to support PSMA as well: Lisa Y Wu, Jacqueline M Johnson, Jessica K Simmons, Desiree E Mendes, Jonathan J Geruntho, Tiancheng Liu, Wessel P Dirksen, Thomas J Rosol, William C Davis, Clifford E Berkman, "Biochemical characterization of prostate-specific membrane antigen from canine prostate carcinoma cells," (Prostate, 74:451-457 (2014)) So, can somebody clarify if PSMA can be indeed a useful biomarker to target in the PC canine model? Thanks!
    Huibert Michiel Vriesendorp · Independent Researcher
    PSA in dogs would provide an excellent translational model for targeted therapies for human prostate cancer. Human prostate cancer is currently treated with some measure of success with surgery and/or various modes of radiation. Both therapies have significant local side effects that significantly decrease the QOL of patients. by damge to surrounding tissues, rectum, bladder and sexual functionalities. PSA as a biomarker in man is confusing and terrifying for patients waiting for the result. PSA is not specufic for cancer and goes up and down like spring weather. Canine PSA could provide a useful target for trageted therapy such as radiolabeled immunoglobulin labeled therapy. Specific murine monoclonal Ig reactive with canine PSA, painted over frozen or formalin preserved canine prostate cancer containing tissues and stained with regular immunofloresence reagents would tell you whether dogs can be treated with RIT and at the same time provide a good model for selecting less toxic, more effective targeted therapies for human patients with prostate cancer.
  • Tanya Guha added an answer:
    How can I accurately quantify circulating DNA (in extremely low concentrations)?
    I have tried using PicoGreen to tried and quantify circulating DNA, however I am not getting accurate results (perhaps because the DNA is so fragmented). Are there any other assays (such as BioAnalyzer) that others have successfully used to quantify such small amounts of fragmented DNA?
    Tanya Guha · SickKids
    Thanks Norman!
  • Megan Yvonne Murray added an answer:
    Can anyone give me some information on scoring methods for IHC slides in myeloma?
    I am staining myeloma samples for the expression of a panel of markers. When it comes to evaluate these slides, I cannot find any exact criteria defined in papers. Can anyone please help me with this?
    Megan Yvonne Murray · University of East Anglia
    Image J (with plugins for Area Calculation) is a great (and free) program that I use for quantifying fluorescent cells and tissues on slides - I see no reason my it wouldn't work for IHC as well. Apologies if you've already covered this - it's quite a long thread! Please reply iF you need more details!
  • Caiyun Luo added an answer:
    What are some useful methods & tools for finding relevant biomarkers for projects?
    With the growing number of biomarkers regularly discovered, going through clinical trials and more slowly translating into the clinic, what options are available to shortlist and find biomarkers? For example for: - Developing new diagnostics/drugs - Researchers seeking to make new biomarker discoveries  - Selecting biomarkers for disease diagnosis/treatment  - other ways biomarkers are used/needed for projects
    Caiyun Luo · China Agricultural University
    Outliers are the goal for biomarker seekers, all the time. The key is how to find out the outliers. With the development of Bioinformation, outliers can be found more easily. However, I don't think all outliers appeared have been researched or noticed. So, reviewing results of others' research may be a way. Besides, new findinds always depent on new technology. If the current technology truly block the further finding, maybe the shortage of them should be improved. another way is broading the area you focus, like the project, namely RIOK, started recently.http://www.r10k.org/R10K/About_R10K.html R10K update: NGS of immune repertoire for biomarker discoveries (P3241)(J Immunol)
  • Deepak Kanojia added an answer:
    What is the amount of Trastuzumab that reaches the breast cancer/metastasis once injected with 2mg/Kg of Trastuzumab in Humans?
    I am looking for the effective amount of Trastuzumab that is responsible for killing the breast cancer cells in Humans
    Deepak Kanojia · University of Chicago
    Thank you for your comments, however I reiterate that I need the effective concentration of Herceptin to kill/inhibit tumor growth. The serum concentration does not tell me how much is effective. I wish to know if there exist any paper where authors measured the "amount" of herceptin/trastuzumab in the human tumors after systemic injection of herceptin. I am asking this because if I wish to "in a way" inject trastuzumab directly to tumors, what is the amount of trastuzumab I should inject.
  • Paul Slowey added an answer:
    How efficient is current non-invasive sample collection vs. blood in genomics downstream applications?
    We, Mawi DNA technologies, have recently developed a new non-invasive sample collection technology that is designed to simplify self sampling and as an more efficient replacement of blood. Please feel to contact mawi at info@mawidna.com if you are interested in evaluating this innovative sample collection in your downstream application. Briefly, The iSWAB-DNA device is equipped with a squeezing insert to enable the efficient removal of swab collected cells/sample in a proprietary stabilizing solution. The innovative design of iSWAB allows for thorough removal of the cells/sample captured by the swab and then release into a proprietary lysis and nucleic acid stabilizing buffer. The combination of the mechanistic release feature and proprietary lysis buffer allows for a high quantity of cells to be collected in a concentrated manner from single or several swabs in a small amount of lysis buffer while maintaining low bacterial contamination. The process enables long term preservation of the sample at the point of collection and is suitable for room temperature storage, transport and extraction. A non-specialized individual can collect multiple swabs in a single device which concentrates the sample without the need of any component of the swab to be included, significantly reducing processing time and costs at the lab. The iSWAB is a self collection device where the whole collection process does not exceed more than 5 minutes and can be performed by a professional or by non-professional (self collection) with equal ease and simplicity.
    Paul Slowey · Oasis Diagnostics Corporation
    Oasis Diagnostics Corporation offers a collection device called the DNA•SAL™ which collects about 180 ng/ml of good quality DNA (~3 ml of sample, so ~540 ng DNA). It can even go direct-to-PCR with a DI water dilution.
  • Hamed Abdelazim Helal added an answer:
    How can I carry out the MTT test with HCC1599?
    I want to measure growth inhibition using HCC1599, but as it is a suspension cell line, I need to remove the medium before I add the MTT solvent without losing cells.
    Hamed Abdelazim Helal · Al-Azhar University
    Thanks alot .... I really approciate your advices
  • Jan Voskuil added an answer:
    Is the efficacy of chemotherapy a biological enigma?
    Based on other discussions, it appears that former claims of efficacy (no matter what therapy) are disputed based on unclear statistic underpinning. One conclusion was that a clinical trial needs an academic mathematics / statistics group involved from design to finish in order to ascertain integrity of the way data are collected and interpreted. This is a call for retrospective evaluation, in particular for claims on chemotherapy. Were all trials conducted appropriately with sound statistics? From a biological point of view, chemotherapy destroys all dividing cells good or bad, and therefore will sooner or later kill the patient by the side effects. Is this biological argument flawed (and if so, why/how), or are the clinical trials claiming efficacy flawed (and if so, why/how)?
    Jan Voskuil · Everest Biotech
    Many thanks for your contribution Huib! I fully agree, even to do simple experiments while not having the complete picture. My concern is that the clinical trials I have been seeing were far from simple and based on premature evidence. I am all for further studies to get better knowledge on how a candidate target is involved in a certain type of cancer. That is different from doing large scale trials on inhibitors to seek efficacy. Anyway, my question still stands on whether historical clinical trials on chemotherapies based on which hospitals prescribe today meet today's more stringent standard. In addition, I wonder to what extend chemotherapies are used for solid tumor treatment, given they seem to have efficacy in liquid tumors only (based on Huib's comment)?
  • Daniela Bruennert added an answer:
    Is it necessary to have the same type of samples in a case control study?
    For an example: I want to study rsxxxxxxx SNP in Indian population. I have FFPE samples obtained from NSCLC patients. Which kind of control samples should I procure? Is it necessarily to be a FFPE samples or normal EDTA blood samples are good enough?
    Daniela Bruennert · University of Wuerzburg
    For this kind of study there is some kind of statistics telling that you need a minimum of 80 vs 80 samples. I know from SNP studies that it's possible to publish data with approx. 50 patients (and 100 patients), but for our ovarian cancer study we trying to publish at the moment we were using approx. 250 patients and 400 healthy controls, using DNA extracted from EDTA blood. If you want to introduce SNPs as molecular markers it is always better to go for a big patients cohort (something like 1000 or even more patients), but initially I would start with 10-20 samples to see if the SNP has any drastic difference. For me, a good molecular marker is a SNP where one allele can found in something like 80-90% of patients whereas the other allele can be found in 80-90% of control group.If you have a big patients cohort (several hundred or thousands of patients) you will obtain fine differences (like e.g. 22.4 vs 26.1%)...
  • Hubert Beaumont added an answer:
    What is the most used technique to calculate chemotherapy dosage?
    What is the most used technique to calculate chemotherapy dosage? What are emerging techniques, including their pros and cons? Can anybody give me a pointer to reference documents?
    Hubert Beaumont · Median Technologies
    Thank you very much for these inputs Dr. Davis
  • Zohreh jaafari-ashkavandi added an answer:
    Can all malignant tumors (cancers) metastasize to other organs?
    Cancers metastasize via seeding through blood or lymphatic vessels.
    Zohreh jaafari-ashkavandi · Shiraz University of Medical Sciences
    No.Metastasis is an very rare event in some malignant tumors for exaple:Bcc,Verrucouscarcinoma,..
  • Jose Gros added an answer:
    I am interested in finding the markers for urinary bladder cancer for diagnosis. Please help me in finding the markers via microarray.
    Working plate form.
    Jose Gros · Sociedad Española de Oncología Médica
    This is the one cited above, connected to your query, but you're the only one in knowing how closely it fits your needs. Salut + Br J Cancer. 2014 Feb 4;110(3):679-85. doi: 10.1038/bjc.2013.744. Epub 2013 Nov 28. Urinary EpCAM in urothelial bladder cancer patients: characterisation and evaluation of biomarker potential. Bryan RT(1), Shimwell NJ(1), Wei W(1), Devall AJ(1), Pirrie SJ(1), James ND(1), Zeegers MP(2), Cheng KK(3), Martin A(1), Ward DG(1). Author information: (1)School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK. (2)1] School of Health and Population Sciences, University of Birmingham, Birmingham B15 2TT, UK [2] Department of Complex Genetics, Cluster of Genetics and Cell Biology, NUTRIM School for Nutrition, Toxicology and Metabolism, Maastricht University Medical Centre, Maastricht, The Netherlands. (3)School of Health and Population Sciences, University of Birmingham, Birmingham B15 2TT, UK. BACKGROUND: Epithelial cell adhesion molecule is overexpressed in bladder tumours and released from bladder cancer cells in vitro. We test the hypotheses that urinary EpCAM could act as a biomarker for primary bladder cancer detection and risk stratification. METHODS: Epithelial cell adhesion molecule was measured by ELISA in urine from 607 patients with primary bladder tumours and in urine from 53 non-cancer controls. Mann-Whitney tests and ROC analyses were used to determine statistical significance and discrimination between non-cancer controls and different stages and grades of disease. Multivariable modelling and Kaplan-Meier analyses were used to determine prognostic significance. The structure of urinary EpCAM was investigated by western blotting and mass spectrometry. RESULTS: Urinary EpCAM levels increase with stage and grade of bladder cancer. Alongside grade and stage, elevated urinary EpCAM is an independent indicator of poor prognosis with a hazard ratio of 1.76 for bladder cancer-specific mortality. The soluble form of EpCAM in urine is the extracellular domain generated by cleavage between ala243 and gly244. Further studies are required to define the influence of other urinary tract malignancies and benign urological conditions on urinary EpCAM. CONCLUSION: The extracellular domain of EpCAM is shed into urine by bladder tumours. Urinary EpCAM is a strong indicator of bladder cancer-specific survival, and may be useful within a multi-marker panel for disease detection or as a stand-alone marker to prioritise the investigation and treatment of patients. The mechanisms and effects of EpCAM cleavage in bladder cancer are worthy of further investigation, and may identify novel therapeutic targets. PMCID: PMC3915119 [Available on 2015/2/4] PMID: 24292452
  • Ulrich Friedrich Wellner 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?
  • Tahmina C Islam added an answer:
    What is your opinion on fewer cancer diagnostic biomarkers vs cancer therapeutic targets?
    I was wondering if there is more ongoing research involving newer biomarkers for earlier detection of tumours. As much as one hears about the newer ongoing cancer therapeutic research or late stage cancer, one doesn't hear or follow much about the newer cancer diagnostic biomarker studies. I would like to get your feedback on this issue. As an example, the overexpression of p16 (INK4a), in initiation of neoplastic transformation of HPV infected cervical epithelial cells has been useful in the early detection of cervical cancer using Immunohistochemistry and has been very helpful in the clinics. On the other hand, targeted molecular research application of cancer therapy for breast and lung cancers, such as HER2/Neu or EGF receptor 1 inhibitors, do reduce the tumours but at that point the tumours are already very aggressive in nature and also such therapies become very expensive for the patient and have a lot more side effects that also limit their efficacy. Also cancer is curable when detected early and prevention is better than cure.
    Thank you for your valuable comments on both aspects, and I would love to get the refs when you complete the project and to be able to add other antibodies for early detection in the clinics at a later point will be very helpful.
  • Shail Kabrawala added an answer:
    Does anyone know of any systematic study looking at importin expression/abundance of alpha isoforms in a tissue specific manner?
    Does anyone know of any systematic study looking at importing the expression/abundance of alpha isoforms in a tissue specific manner?
    Shail Kabrawala · University of Connecticut
    Thank you very much
  • Octavian C Ioachimescu added an answer:
    How to calculate local tumor burden in pleural effusion in lung cancer?
    I am carrying out research on evaluating novel drug efficacy in pleural effusion in lung cancer. I feel that local tumor burden could be an important prognostic factor. How should I then eliminate the influence of local tumor burden? Thanks.
    Octavian C Ioachimescu · Emory University
    Malignant cell crit, pleural fluid/serum glucose ratio and PET scan combined sound like the best combined way to asses; keep in mind that certain tumors may invade pleural layer without shedding a lot of malignant cells into the effusion, hence PET scan of the pleural rind plus SUV of the pleural effusion may take you somewhere...
  • Pawel Buczkowicz added an answer:
    How to perform a tissue-based diagnosis if a tumor biopsy is not feasible?
    Is it possible using molecular imaging technique or what else?
    Pawel Buczkowicz · SickKids
    It is possible and in fact standard practice for certain cases, like for a type of brain tumour called DIPG, where biopsies are rare (because of location within the brain) and diagnosis is done based on MRI and clinical presentation, such as duration of symptoms. However, whenever possible I believe that a tissue biopsy is always beneficial for confirming or determining a diagnosis.
  • Karima Akool Al-Salihi added an answer:
    Does the presence of TGFb in serum induce fibrosis in organs?
    We know that TGFb is a profibrotic factor. Does the presence of TGFb in serum induce fibrosis in organs? Can anyone suggest an article where it shows the presence of high levels of TGFb in serum induces fibrosis in organs such as liver, lungs and kidneys?
    Karima Akool Al-Salihi · http://scholar.google.co.uk/citations?user=JyubnQQAAAAJ&hl=en
    Another article
  • Aref Sobhkhizy added an answer:
    How can I isolate the blood plasma without degradation, precipitation and/or loss of microRNAs of the blood?
    What's the best protocol to isolate the blood plasma in order to save all microRNAs of the fresh blood?
    Aref Sobhkhizy · University of Tabriz
    dear Kenneth : thank you
  • Thao Huynh duy added an answer:
    Is there any way to determine abnormalities in the cultured mesenchymal stem cells in vitro?
    Is there any way to determine abnormalities in the cultured mesenchymal stem cells in vitro? If I would only use karyotyping, there is insufficient evidence to determine the safety of the cell.
    Thao Huynh duy · Pham Ngoc Thach University of Medicine
    Thanks Carmen Hoz a lot. I hpe we'll discuss more in the future. Thanks again.
  • Nathan R. Wall asked a question:
    How long are exosomal surface proteins stable at -80C?
    Exosomes in our hands are stable as defined by nanosight analysis. However, by Western blot analysis, exosome surface proteins appear to disappear in a time-dependent manner. Has anyone else observed this phenom and how have you handled it if you have?

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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