Science topic

Colorectal Cancer - Science topic

This group deals with the genetic aberrations in the Signal Transducing Molecules involved in the development and progression of colorectal cancer.
Questions related to Colorectal Cancer
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I measured the protein expression of β-catenin in CRC organoids on
different days, but the molecular weight of β-catenin was different on day 7 and day 14.
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This may not be the answer, but have you considered different PTMs of β-catenin?
It might also be easier to interpret if you include the molecular weight ladder in the image. How much is the difference between day 7 and 14?
Best of luck!
Sam
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We need your expertise & opinion!
Please fill in this questionnaire:
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Is best to prevention also to treatment.
The best test option for screening of CRC is FIT test and consecutively colonoscopy.
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I´m having some trouble growing CRC organoids from biopsies (maybe with low tumor cells present).
Is there any trick that could improve the growth of CRC organoids from biopsies?
Material and methods I´m currently using:
Biopsy digestion medium:
1.58 mg/ml collagenase type II ,
10 ug/mL of hyaluronidase Type IV
100 ug/mL primocin
10 µM RhoKi
Basal expansion medium for CRC organoids (WNT is omitted):
  1. AdvDMEM+++ (see recipe)
  2. 1× B-27 Supplement
  3. 20% (v/v) Rspo1-CM
  4. 100 ng Noggin
  5. 1.25 mM N-acetylcysteine
  6. 10 mM nicotinamide
  7. 10 μM p38 inhibitor SB202190
  8. 50 ng/ml epidermal growth factor
  9. 0.5 μM ALK5 inhibitor A83-01
  10. 1 μM prostaglandin E2
Extracellular matrix:
1. Cultrex BME (R&D)
Passage:
TrypLE + Rhoki
Refresh medium every 2-3 days
Passage every 7 days.
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Dear Paolo,
Thanks for your reply. At the moment GrowDex is for research use only but I'll let you know when GMP grade hydrogel is available.
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Each taken gene ontology for dysregulated genes set in colorectal cancer has a biological function in neurogenesis. Can anyone explain why?
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Articles remark that cells plated at the right density have enhanced efficiency of organoid culture establishment. Plating too densely will result in increased cell death at the core of the dome.
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Dear Melis.
I have established CRC organoids even with 2x105 cells per 20 uL in a 12-well plate (usually 5-6 domes of 20 uL matrigel). If we go for 1000 cells per 20 ul it will be millions of plates and a lot of matrigel, as normally we get resection tissue and we collect around 1x106 cells after digestion. In fact, larger density is better as shown in this link (at least for mouse organoids).
Remember to put the plate up-side-down during polymerizing the matrigel to ensure that the cells stay in the top of the dome. There is no doubt that low cell density is not good either, so try to titrate your cells in different densities and evaluate the growth rate and diameter.
Good luck.
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After low or ultralow anterior resection, it is difficult to assess the future bowel function before reversing the ileostomy
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Schwandner F, Klimars U, Gock M, et al. The Water-Holding Procedure for Ensuring Postoperative Continence Prior Restoring Intestinal Continuity. J Gastrointest Surg. 2020;24(2):411-417. doi:10.1007/s11605-019-04171-7
A standardized water-holding test can function as an easy and reliable method before stoma reversal to predict sufficient postoperative fecal continence. In case of a sufficient water-holding test despite low manometric pressure levels, the risk for postoperative anal incontinence seems to be low. Preoperative manometric pressure levels do not appear to predict postoperative continence.
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Dear Colleagues
We injected CT26 cells into rats' flank (s.c) to induce colorectal cancer. What biochemical tests do you suggest (sensitive ones) to ensure that animals are bearing tumors? I mean, is it possible to ensure with high blood glucose, FOBT tests, etc., that animals have colorectal cancer before doing sophisticated techniques such as PET-Scan or MRI (mainly because of their cost). We finally will do them, but we just weren’t to be ensured that animals have a tumor. I should mentioned that after 10 days of CT26 injection no macroscopic sign is detected in animal so far.
Thank you for sharing your experience
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Unfortunately, there’s no reliable way to do this with any current biochemical method.
Hopefully, this will become possible in the future.
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I am analysing data for colorectal cancer study
Among the data
I have 3 columns
Chemotherapy yes/no
Radiotherapy yes/no
Surgery yes/no
..
and i have years of survival
..
I want to know the relation between years of survival and type of management
i.e. which one of them has the highest years of survival
Note: some patients used more than one type of management
..
What is the best way/test to do this??
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I would suggest a one way analysis of variance of survival time by treatment type ie C, R, S ,C+R, C+S, R+S, C+R+S .
Then do comparison of means , taking account of the multiple comparison problem by a standard method.
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Hi! Our lab is working with primary cancer cells from colorectal cancer and on the weekend the CO2 ran off from the CO2 tank. Some cells are dead, but some are alive. However, I believe that they feel bad. I want to recover alive cells. How to do it?
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I read an article for Colorectal cancer that evolves through a stepwise accumulation of genetic and epigenetic alterations, leading to the transformation of normal colonic mucosa into invasive cancer.
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Describing the exact pathway or pathways to be more exact, the classical CIN, MIN and CIMP models are proposed; going for the exact trigger and subsequent promoter pathways is a research subject, can be done by gene sequencing, ihc and other modalities. In Sporadic CRC rarely we require such a thorough workup except for All RAS, Her2, BRAF mutations, in metastatic CRC.
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Hi! Our lab just starts working with colorectal cancer organoids and breast cancer organoids. And we faced the problem in freezing of organoids.
Currently, we use such protocol: organoid pellet is resuspended in the 1ml of freezing medium, which contains 20% of DMSO and 80% of FBS, then we put the cryovial in Mr. Frosty Freezing Container overnight, and on the next morning we put the cryovial in the liquid Nitrogen. For the unfreezing, we put the cryovial in the incubator (+37 ℃) for a few minutes, while there will leave only a small piece of ice (with size as a pea), then transfer the cryovial to the hood and add the content of cryovial to the cold DMEM by drops. Additionally, we are shaking the tube with a DMEM while adding the organoids. Then we centrifuge for 5 minutes on 450 × g, 4°C, remove the supernatant, and seed the organoids on the Matrigel. Additionally, we are adding the CHIR-99021 and Y-27632 to our medium. However, after few days we are noticing that everything is dead.
What we are doing wrong? Maybe we should change somehow the freezing medium? Could you please recommend a working freezing protocol for organoids?
Thanks in advance!
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20% DMSO seems rather high; I typically cryopreserve cells [suspension, not organoids] in 10% DMSO/90%FBS. I would suggest trying 10% DMSO/90% FBS.
The issue is that DMSO permeates into the cell, and even at 10% is hypertonic [~.375M vs ~.165M for normal saline], so 20% would be even more so. Upon thawing and dilution, your organoid cells may be rupturing from the influx of water due to the DMSO inside the cells.
Upon thawing, I always add my thawed cells into a tube of either HBSS or medium underlayed with 1 ml FBS. This seems to improve recovery.
Hope this helps.
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Is palliative surgery of total colectomy and removal of rectal mass (not curative) associated with an increase in progression-free survival of patients with metastatic colorectal cancer? has anyone seen a paper or textbook in this regard?
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Perhaps it is necessary to consider each situation individually, and everything will depend on the tumor process, the patient's status, the goal that the operation will pursue… Ultimately, the goal of treatment is to help the patient, and in every situation you need to think about it, it will depend on whether you need to operate or not, what kind of operation will be.
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I am working with rectal swab samples in the field of colorectal cancer research. Does anyone have experience (or can point towards any relevant literature) of specifically working with proteins (extraction, characterization, or anything even remotely connected to protein work) in rectal swab samples (or any mucosal swab samples).
Thank you!
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Hi Colleague
Find the paper at the following URL may help you:
Regards...
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I have carried out a dietary questionnaire for the nutritional prevention of colorectal cancer, so I evaluate the amount of fiber consumed daily using a simple food frequency questionnaire. As well as the consumption of red meat and processed meat in order to offer nutritional advice adapted to the personal consumption of patients at risk of colorectal cancer. Patients are seen again a few months after to re-evaluate their consumption. Although most patients increase their fiber intake, it is quite disappointing for them not to reach the recommended 30g of fiber per day or at least 25g for women or the elderly. I was therefore wondering if there was a curve showing the health benefits or more specifically colorectal cancer benefits as a function of fiber intake. This would allow me to estimate the percentage benefits on overall health or colorectal cancer of an increase in fiber intake. Thank you in advance.
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The average adult only eats 15 grams of fiber per day.
Women need 25 grams of fiber per day, and men need 38 grams per day, according to the Institute of Medicine.
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I am planning to use a 96-well format for an experiment as this will greatly improve throughput and expedite treatments. I will be using Caco-2 cells cultured apically. I need them to form confluent, differentiated monolayer on the insert. Do you have any experience doing this in a 96-well format? What are the difficulties you have encountered? Thanks!
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I've tried doing something similar (transwell 96-well). The edge effect was the biggest problem. Another issue I can foresee in your experiment is testing the permeability of each of the monolayer (96). If the integrity of some of them isn't good then you would have to avoid those wells and it might make the assay design confusing. Anyway, good luck.
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Hello everyone.
Based one the papers that I've read, GAPDH seems to be overexpressed in colorectal carcinoma. Other than GAPDH,  what are the best housekeeping genes that I can use for expression studies in human colorectal system
Thank you in advance! 
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"In chronic inflammation, IL-6 has a detrimental role that favours mononuclear cell accumulation at the site of injury, through continuous MCP-1 secretion, angioproliferation and anti-apoptotic functions on T cells [30]. This may increase serum levels of IL-6 and provide the basis for the amplification step of chronic inflammatory proliferation."
Interleukin-6 is released by monocytes and macrophages in response to other inflammatory cytokines which include interleukin-11, and tumor necrosis factor (TNF)-beta.
"Chronic inflammation can result from the following:
  1. Failure of eliminating the agent causing an acute inflammation such as infectious organisms including Mycobacterium tuberculosis, protozoa, fungi, and other parasites that can resist host defenses and remain in the tissue for an extended period.
  2. Exposure to a low level of a particular irritant or foreign materials that cannot be eliminated by enzymatic breakdown or phagocytosis in the body including substances or industrial chemical that can be inhaled over a long period, for example, silica dust.
  3. An autoimmune disorder in which the immune system is sensitized to the normal component of the body and attacks healthy tissue giving rise to diseases such as rheumatoid arthritis, systemic lupus erythematosus (SLE).
  4. Recurrent episodes of acute inflammation. However, in some cases, chronic inflammation is an independent response and not a sequel to acute inflammation for example diseases such as tuberculosis and rheumatoid arthritis.
  5. Inflammatory and biochemical inducers are causing oxidative stress and mitochondrial dysfunction such as increased production of free radical molecules, advanced glycation end products (AGEs), uric acid (urate) crystals, oxidized lipoproteins, homocysteine, and others."
Cytokine Panel (ARUP):
Interleukin 2 Receptor (CD25) Soluble
Interleukin 12
Interferon gamma
Interleukin 4
Interleukin 5
Interleukin 10
Interleukin 13
Interleukin 1 beta
Interleukin 6
Interleukin 8
Tumor Necrosis Factor - alpha
Interleukin 2
Interleukin 17
Question:
If CRC patients had a hair sample analyzed for fungal cultures, what fungi would be found?
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Bogdan Socea Thanks for sharing - I agree!
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I'm using Abcam 112116 cell cycle assay kit - Green Fluorometric to detect cell cycle for HCT116 and Caco2 (colorectal cell lines). I've performed an optimization run using the recommended protocol (Nuclear green 1:200), and I even included several nuclear green concentrations (1:400, and 1:600).
Cell scattering shows two populations for HCT116 (probably cell duplicates) and minimal separate scattering with Caco2 (for 1:200 only as recommended by the kit). Nevertheless, when I select a single cell population I can't seem to see a normal cell cycle, always one prominent peak is showing.
What could cause the disappearance of cell cycle?
Note the following:
- Untreated unstained samples were used to detect auto-florescence
- Untreated stained cells were used to detect normal cell cycle
- I've used a cytotoxic treatment below IC50 for 24 hrs duration
- Treated stained cells are being investigated for cell cycle arrest compared to untreated ones
- Floating treated cells were collected in the samples
- Floated untreated cells were NOT collected in the samples
- no starvation was done
- Incubation of cells with nuclear green was 50 minutes
- cells are adherent, so trypsinization was done and following by complete media wash prior to incubation of with nuclear green in fresh complete media
- I've used Doxorubacin as a sample, the graph shows shifting but I can't quantify it without distinct cell cycle phases (attached is a full profile scatter for dox).
Should any of the following suggestions be crucial for better cell cycle presentation:
- Starving the cells prior to treatment?
- Using short duration treatment (<24 hrs)?
- Using low passage cell line? avoid advanced passage cell lines?
- Using IC50 or above IC50 concentrations of cytotoxic agents?
- Using higher dye (nuclear green) concentration (>1:200; recommended is 1:200)?
- Using prolonged incubation time with the dye (>60 minutes; recommended is 30-60 minutes)?
- Using cell strainer to avoid duplicate cells?
- Floating cells in the treated/untreated samples should/not be collected?
Attached is a full scattering profile for the untreated HCT116 cell line. Note that the second peak is probably representing cell duplicates rather than a population of single cells in the G2 phase, despite using a cell strainer.
Thank you
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Hi Husam,
Have you contacted Abcam's tech support?
One other thought is that the cells might have the capacity to clear the Abcam probe (drug resistance mechanism). Perhaps adding 0.5% formaldehyde would "snap" the pumps involved in this without permeabilising your cells or affecting the expression of other cell surface markers. PI will not suffer from this because of the fix, perm, RNase procedure required to use it.
Regards,
Roy
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What are the new markers used as prognostic markers for colorectal cancer ?
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You might this paper interesting
Cancers (Basel). 2020 Feb; 12(2): 319.Published online 2020 Jan 30. doi: 10.3390/cancers12020319PMCID: PMC7072488PMID: 32019056
Prognostic and Predictive Molecular Biomarkers for Colorectal Cancer: Updates and Challenges
Eric Koncina,1 Serge Haan,1 Stefan Rauh,2 and Elisabeth Letellier1,*
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Dear Authors.
I have a novel and original project about the role of ligand in activation of STAT 5 in cancer,
Currently I'm looking for a PhD supervisor are interested in this project and can supervise it as PhD supervisor to discuss with you.
Best Regards
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Congratulations for your interesting research topic, unfortunately not within my fields of interest. Sicerely, MGiuliana
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We would like to evaluate a blood testing device for serial monitoring (ideally 3+ times in different cancer stages per patient). We couldn't find a blood bank that stores a series of samples for prostate and colorectal cancers... Is there any?
Thank you.
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I recommend you to search hospitals for patients of colorectal cancer and prostate cancer otherwise I don't think you will find this samples at blood bank.
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I have found stage zero or intramucosal carcenoma or carcenoma in situ of colon and rectal cancer is under studied. However, an expert may guide me better understanding: why it is under studied? Is the risk of death too low, or is  disease prognosis very benign?
I appreciate your answer that might shed lights on it.
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By using RT-PCR & IHC techniques, What are the best markers used for early diagnosis of colorectal cancer as prognostic markers rather than KRAS gene?
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"In conclusion, high-dose intravenous ascorbate represents a promising and inexpensive anticancer therapeutic option that should be further explored in clinical trials. Given its low toxicity and low financial cost, ascorbate could become an important weapon in our arsenal against cancer, either acting as a single agent with predictive biomarkers or used in combination as an adjuvant therapy."
Targeting cancer vulnerabilities with high-dose vitamin C
Bryan Ngo, Justin M. Van Riper, Lewis C. Cantley & Jihye Yun
Nature Reviews Cancer volume 19, pages 271–282 (April 2019)
Invitation: Start a clinical trial.
There are currently 15 clinical trials. See details of those trials here: https://www.nature.com/articles/s41568-019-0135-7/tables/1
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Joe Graymer
Gamal Abdul Hamid Luis Rodrigo Wolfgang Doerr , check this out:
Alessandro Magrì et al. High-dose vitamin C enhances cancer immunotherapy, Science Translational Medicine (2020)
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Questions to consider: (1) Do we find evidence of certain bacteria overpopulating/underpopulating in patients diagnosed with colorectal cancer? Are they inhibiting or contributing to cancer cell proliferation and growth? How would we measure that?
(2) "It is now recognized that the gut microbiota and chronic liver diseases are closely linked." Would we find evidence of liver dysfunction/malfunction in those diagnosed with colorectal cancer? ( Quote from paragraph entitled "Liver disease and the gut microbiota" in .)
(3) If the 3 ‘P's’ for gut health are probiotics, prebiotics and polyphenols, then what effect, if any, would a SIGNFICANT increase in one of these have on a colorectal cancer patient's length of survival?
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Hi Samy Azer thank you for sharing and reaching out! I currently am not doing a research project on this. When you suggest I submit a method study, are you suggesting I summarize current methods and their effectiveness (e.g., a lit review)?
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My research specifically looks at the colorectal tumor's adjacent normal tissue and its small RNA (mainly miRNA) expression and its role as a prognostic marker. Currently I wish to interrogate data from web repositories such as TCGA and evaluate the expression of a few miRNAs that I am interested in?
The problem that I however face is that there are extremely few adjacent normal tissue expression data for miRNA or mRNA in resources such as TCGA for colorectal cancer, making them unsuitable to have a statistically strong cohort for evaluation purposes. Could the research gate community guide me to suitable resources or perhaps suggest alternatives to better approach such an evaluation.
To be clear - (a) I am looking at specifically tumor tissue adjacent normal tissue data, and not a healthy normal based data. This is because I am looking at the tumor micro-environment which will not be available in a healthy individual. (b) I have already identified potential miRNAs through my own analysis of patient samples. I wish to perform the above mentioned analysis to have a stronger validation of my dataset. (c) Blood based expression data for the CRC patients is not suitable for my study.
Thanks.
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Hi, I am working on a tumor microenviroment project recently and facing the similar problem. I tried GEO but the data is limited. Most dataset includes more tumor tissue data than tumor adjacent tissue. I wonder whether you have solved this yet?
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When i get the Azoxymethane (AOM) i have stored it at -20. Before use i diluted it with %0.09 SF. After diluting i store AOM at -20 C again. In this condition, does AOM work or not ?
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Would you please inform me, how should prepare AOM for IP injection to mice?
We should dilute it in dH2O?
How much should prepare the final volume for IP injection?
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Dear Scientists,
I am working with a gene of interest in colorectal cancer, which has no role in cell proliferation. In addition, by knockdown this gene, the FAK and SRC protein expression are decreased. I have changed amino acid by SDM and check the protein expression of the gen by WB, the expression is decreased and the MW was less than actual MW. Then, I check the cell proliferation after transfection with mutated plasmid and wild type plasmid, I have noticed a significant increase in proliferation of the mutated one compare to WT. Can anyone have an idea to explain how this is happening?
Thank you in advance,
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Hi Colin,
Can you please explain what do you mean by ''Receptor and expression factor dilution upon division?''?
Thank you,
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Robert John Wolff Yes! Please write this paper and send it to me when you're done. I'd appreciate reading more on this topic and seeing more articles and papers published on this topic.
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Hej,
I have been using Tyramide a lot for both human FFPE and frozen mouse tissues. I have had always good results with these tissues.
I am struggling to use the Tyramide systems in frozen human colorectal cancer tissue though. We freeze the tissue non-fixed and just fix the sections with 2% formaldehyde for 10 min before staining it. I am always getting a strong staining on polymorphonuclear cells because of their endogenous preoxidases. The problem is that no matter how long I block it with H2O2 or NaN3 (or combined), it never disappears and seems to be reversible. Somebody any experience with that? I want to stain MAIT cells and there are no antibodies for FFPE .... Thanks!
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Hi Louis,
FFPE-related material of interest for you:
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I have a lot of new cases of colorectal cancers between 2005 and 2010. I calculated age-specific incidence rate for each year (from 2005 to 2010). Now, I want to calculate the incidence rate for all then years which should be just one value.
How can I calculate it?
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Dear Mehdi
To calculate average annual incidence rate (single value for the ten years), there is a simple method
1. You add all cases registered in the ten years and obtain their average
Summation of cases in 10 years
Average number of cases =---------------------------------------------------------= A
10
2. Obtain the mid-period population by either similar method to 1 above or
just take the average of the population in the middle two years ( population of 2007 +population of 2008) divided by two = B
A
The average annual incidence rate =--------------- X100000
B
With best regards
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Hi, there,
I am doing primary culture of colorectal cancer. In recent months my cultures are contaminated. I suppose it is some kind of bacterial. It grows slow and almost always appears after 4 days of culture. It doesn't move a lot and forms single clones on the surface of the plate. The culture media turn yellow easily. The micorbie is penicillin-streptomycin resistant. No antifungal drugs have been tried.
Almost everything has been checked to find out and to remove the contamination. The culture media, digestion enzyme and PBS had been cleared. When they were cultured alone, there was no contamination. It is not caused by the tissue, because when I tried to culture cell lines or other materials, the problem persists. It's probably caused by the incubator. I used a Heracell 150i incubator. I changed a new filter and run the autoclave procedure several times, but the problem still exists. I have tried different cultures more than ten times, but the problem always persists.
Anybody have any idea of what could it be and how to solve this problem? Any help will be greatly appreciated. 
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Dear Wei Chen,
It is highly appreciable that you provided supportive evidence (photo) of your problem. Since, you are using Heracell 150i, the shelves are electroplated with stainless steel. Steel accumulates bacteria, dust and fungi. Also, the inline filters if not changed can transmit contaminants. Just by changing HEPA filters do not eradicate contamination. Finally, the purity of CO2 needs to be checked in house. If O2 cylinder is attached, it favours contaminants.
Let me suggest you the way what I follow:
1. Switch off the instrument
2. Disconnect the gas supply
3. Remove sensors ( discard HEPA and inline filters, discard water from tray)
4. Switch on the instrument
5. Run contra con decontamination (90 degree centigrade) - overnight
6. Switch off instrument
7. Replace sensors
8. Fumigate with KmNo4 overnight (along with lab fumigation)
9. Remove fumes periodically (2 days)
10. Wipe the entire incubator, tray and shelves with 70% ethanol
11. Replace new Filters
12. Fill about 1 liter of water in tray and add 2-4 gms of CuSo4
13. Check the sterility of instrument with open blood agar, SDA plate and Thioglycollate broth
14. Wait for one week (but, change water in the tray once or twice per week)
15. When result is negative, use the incubator after wiping with 70% ethanol.
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Some studies showed good results after combined therapies (transarterial chemoembolization plus RFA) in hepatocellular carcinoma and liver mets from CRC. We have in selected patients with large tumors who achieved great reductions in the contrast-enhanced areas, and some of them changed their tumor grading.
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Usually we use them sequentially, when needed. However should be careful for the risk of infection
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Though, CRC is constantly increasing in south east Asia due to various factors such as food habits, etc., I'm expecting answers in diagnosis and treatment.
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Good
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I have to collect colorectal cancer tissue that I will section later but I would like to know which one is better, freezing it in liquid nitrogen or in OCT?
Another thing, do I use cryostat or wax(paraffin)? Which one is most preferable?
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Hello everybody
I am going to set an experiment to compare expression of some cancer biomarkers in colorectal cancer cell and normal colorectal epithelium. But unfortunately normal colorectal epithelial cells (CRL1459 &1831) are not available around us. Does anybody have any experience to use human fibroblast cells as a model instead of normal epithelium?
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Where from I can get NCM 460 cell line?? Please suggest
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How do you approach circumferential suspicious Polypoidal mid Rectal lesion which yield high grade dysplasia by 2 different senior endoscopist?
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According to the Paris classification, lesions greater than 2.5 mm in height are considered polypoid. Two attempts of biopsies have already proved HGD. Therefore, polypectomy would be the next step. Biopsies should be used with caution, since they can cause fibrosis in the biopsied area and thus, prevents endoscopic resection. Chromoendoscopy, EUS or MRI should be considered for the estimation of submucosal invasion of the lesion. EMR/ESD could be the option depends on the depth of invasion.
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I want to transfect two cell lines of colorectal cancer (SW48 and HCT116 ) with calcium phosphate transfection method . I couldn't find any paper which work this method for these cell lines i wonder if calcium phosphate transfection method is efficient for SW48 and HCT116 cell lines'transfection?
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Hi,
I suggest you to try lentivirus, which would infect colorectal cancer cell lines very well.
You could find useful information of lentivirus on this website: www.genemedi.net/i/lentivirus-packaging
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Ocotype Dx for breast cancer is 21 gene signature model with 5 house keeping genes and other genes associated with other carcinogenic properties to provide a net score of cancer risk.
Anyone having more experience/information/guidance about its usage ?
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In what sense(s) are you interested in prediction:
1. prediction in presence of disease now in an individual;
2. prediction of future development of disease by risk factors but no disease now present;
3. other senses of prediction?
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In this article fig. 1. The Author has made a decision tree with 24 nodes. Each node is specified for a specific cancer tissue of origin and the couple of MicroRNA which can identify these cancer tissues of origin. My question is, if I isolate miRNAs at the node14(hsa-miR-21, let-7e), node21(hsa-miR-205, 152), node24 (hsa-miR182, 34a, 148), node10(hsa-miR-194, 382, 210), will it be enough to identify cancerous tissue originated from the lung.
Why am I asking this question, because, I want to identify cancerous tissue, which has migrated to different region but originated in the lung. So if I take miRNAs from those specified nodes, will it be enough to identify lung cancer tissue, which has migrated to different region but originated in the lung.
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microRNAs have to provide potential signature model for various cancers and other diseases. While miRNA in terms of sequencing is difficult , though being done provides huge number of miRNA in a specific cancer as you have exemplified some in your discussion. Few important learning points:
1- Specific sets of miRNAs usually express or otherwise together and they are termed miRNA families.
2-Some miRNA have the potential to act as pan cancer biomarkers but still no specificity is provided.
3-Some biomarkers are like positive or negative acute phase reactant and may rise or fall with non-cancerous disease.
4-There is some but as i experienced little correlation between blood and tissue based miRNAs
5- The science of miRNAs is still emerging and a lot more has to be learnt i guess before they are available, if available for clinical use.
6-Also need to have complete data about pre, pri and miRNA and he cleaving proteins like DROSHA, DICER and factors incorporated in RISC complex.
The whole picture is yet to appear and but hope is there that someday they may be appearing as both for diagnostic use and therapeutic targets like Riversin (spelling ?) for treating hepatitis C.
So potential is there but more research is needed to quantify and deal associated aspects of miRNA
Sorry, that I could not help you straight as i interpret the knowledge about this subject is still evolving.
Kind regards
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Colorectal cancer treatment is always a challenging one. Poor diagnosis and later treatment frustrates the CRC patients.
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Hello! Take a look at this paper by NCCN guidelines: https://www.nccn.org/professionals/physician_gls/pdf/colon.pdf
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I would like to isolate cell membrane proteins from human colorectal cancer cells (HCT-15) and human leukemia cells (HL-60). I am in search of a suitable protocol. I have to order all the materials and reagents for this experiment, as in our lab, we are doing this for the first time. So an easy protocol will be preferred. Please share you expertize with me. I will be grateful.
Best Regards!
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Can anyone help me with my research (mRNA expression of Caspase-3 on colorectal cancer) please?
I need help to understand my results.
Thanx in advance
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Thank you
normal group has low level of caspase-3, does it right?
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i need to know aboute the way of opoptosis of colorectal cancer
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Hej,
we are struggling with T-Bet flow cytometry staining for lymphocytes from human colorectal cancer tissue. We are getting a good staining from PBMCs but no positive cells from the tissue. We have tried different kits for transcription factors (ebioscience, BD) as well as different antibody clones. Furthermore, we have exposed the PBMCs to the same digestion enzymes like the tissue cells and T-Bet is still detectable. Any suggestion about a different protocol or Fixing/ staining times/stimulation? Thanks!
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Thanks for your answer. I guess we will need to go with another method too.
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Radiotherapy in Colorectal cancer
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Radiotherapy increases ROS. These radicals induce stress and finally apoptosis. If you decrease ROS with scavengers you will attenuate the effect of radiotherapy. The answer, therefore, is no, there is no benefit using scavengers.
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Hi Friends,
I have found expression of a gene ( continuous variable) is associated with prognosis in colorectal cancer from 7 different datasets a by logistic regression. Thus, I have 7 odds ratio from different dataset. How can I calculate the 'pooled odds ratio' for this gene from these 7 individual odds ratio?
Best,
Nirmalya
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In this case, the datasets should be pooled and run as a single data set. That is the only way you can pool the ORs. I am attaching a paper on a related issue that you may find helpful. Best wishes, David Booth
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Question- Cetuximab is an epidermal growth factor receptor (EGFR) monoclonal antibody used to treat head and neck and advanced colorectal cancer. What are the potential ocular toxicities associated with the use of this drug?
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Dear N. Belloumi
Thank you for your concern. Yes, that's the question!
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I've done several techniques to transfect shRNA-containing plasmid into A549. The techniques that i've done including calcium phosphate, lipo 3000, neon transfection. Now i planned to try electroporation but couldnt find any literature that already done electroporation on A549. Have anyone try this before? I need the parameters; voltage, no. of pulses, pulse duration, cell density
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If you're having problems with transfection efficiency I would recommend finding a transfection reagent specific to A549 (https://altogen.com/product/a549-transfection-reagent-lung-carcinoma-ccl-185/). Electroporation is generally only more efficient in suspension cell lines like Jurkat, but for lung cancer lipofection is generally going to give better results, especially with pre-optimized protocols.
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Genetic testing for hereditary cancer predisposition:
what are studies (or guidelines) focused on panels of genes for breast cancer, ovarian cancer, colorectal cancer and polyposis?
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Hi Tatiyana
some key points you are searching for are focused at:
hue this helps
fred
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I am studying smoothened protein expression on FFPE colorectal cancer blocks. In my IHC experiments I am using abcam anti-smoothened primary antibody and IHC kit. I followed all standard protocols . This protein is a GPCR like protein and is localized in cytoplasm and membrane. However in addition to cytoplasm nucleus were also stained. Iam a bit confused by these results.How can it be present in nucleus. I am new to IHC and dont have much knowledge of this technique . Any advice would be helpful
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Thankyou mir khurshid
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Hello !
Do you know any cancer genetic database where I can get some prognostic and survival data (Kaplan Meier plots) from large prospective studies regarding genes associated with colorectal cancer ?
Thanks in advance !
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International cancer genome consortium is underway in more than 20 countries and it is evaluating genome of various cancers. You may contact and register on site and then specifically contact organisation for support.
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We are looking for potential MSS as well as MSI that clinically resembles CRC. The APCmin mice look promising but many develop, particularly in the small intestine and resemble FAP.
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Spontaneous initiation, promotion and progression of
colorectal cancer in the novel A/J Min/1 mouse
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Can someone please suggest me some research articles for the detection of lung and ovarian cancer using Surface plasmon resonance (SPR)? I found lot of research papers on prostate, breast and colorectal cancer detection, but found only one article for lung cancer (V. Sahu et. al. 2016) and one on ovarian cancer (J. Yuan et. al. 2012) detection using SPR.
I am only interested in SPR detection method.
Thanks in advance!
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Dear Shawana
You may find this article useful
Talanta. 2011 Oct 30;86:377-83. doi: 10.1016/j.talanta.2011.09.031. Epub 2011 Sep 22. Surface plasmon resonance based immunosensor for the detection of the cancer biomarker carcinoembryonic antigen.
Altintas Z1, Uludag Y, Gurbuz Y, Tothill IE.
Good luck
Sivakumaran
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Hello to all,
I want to do a cluster analysis for colorectal cancer data. For this purpose, I've created a 100*100 Fishnet layer for study area. I know that I can do spatial join to calculate the number of points for each of rectangles but I do not know how can I add population data?
I need population data for calculating incidence and prevalence of disease for each rectangle.
Thank you
Behzad
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Dear Abdallah,
Thanks for the links. I have studied them but they have not mentioned anything about GIS analysis and Fishnet. They are about incidence, prevalence and some other epidemiological measures. I know how to compute the prevalence and incidence. My problem is the population. I do not have population for Fishnet analysis.
Thanks
Behzad
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I want to make a list of 150 western blot ABs to screen for interesting mechanisms/pathways in CRC cell lines (HT29 and HCT116 which we will treat with some drugs). Which pathways should be considered? Which ABs should I look at for assessing the pathways?
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Hi Leonhard
you can read this paper:
Colussi D, Brandi G, Bazzoli F, Ricciardiello L. Molecular pathways involved in colorectal cancer: implications for disease behavior and prevention. International journal of molecular sciences. 2013 Aug 7;14(8):16365-85.
Best
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Hi everyone,
I have the age adjusted rates of colorectal cancer for 12 years from a region. I need to make a comparison between two periods and I am not sure which test to use in SPSS. I would be grateful to have your ideas.
Thanks
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Dear Dr.Sharifi,
It is my pleasure to have your reply,
It was of great help for m, specially using Epi info for comparing the rates is more practical. Thanks again for recommending.
Regards
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After the RNA isolation from fresh colorectal cancer biopsies, I dose my RNA's concentration, and I find about 3000µg/ml. In RT, I take 5µl of my RNA at 1ug :
Ci= 3000 µg/ml
Cf= 200 µg/ml (1µg/5µl)
Vf= 50ul
then I found Ci= 3,3 µl from my RNA + 46,7 H2O
I would ask if someone knows if I can use a concentration of RNA higher than 1µg??
Thanks.
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Agree with @ Ali Mahmoudpour
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I am looking for an equivalent of the MCF10A for breast for EMT-induction studies.
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Caco-2 cells are colon cancer cells and not normal. The CCD-18co are fibroblasts.
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Hi every body
I work on Wnt/beta catenin signaling pathway. I have a drug which is effective on non metastatic SW480 cell line. I want to test it on metastatic cell line SW620. the pathway is active in both cell line and the drug inhibited the pathway. so it is resealable that i expect the drug have some effect on SW620?
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For Wnt signaling in SW480 and SW620 cells, the following papers may be useful:
NaBt (sodium butyrate, HDAC inhibitor)
Emodin (anthraquinone)
OVOL2 (member of the Ovo family of conserved zinc-finger transcription factors)
XAV939 (Tankyrase 1 inhibitior)
microRNA-195
MicroRNA-27a
microRNA-145
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Accumulating evidence demonstrates that intestinal bacteria influence oncogenesis, tumor progression, and response to therapy. Thus, selectively manipulating the gut microbiota may represent a feasible means to (i) limit the incidence of specific tumors in the general population and/or (ii) improve the activity of various anticancer agents . Although the first possibility has been investigated in several models of oncogenesis with promising results, the actual oncopreventive effects of anti-, pre-, pro-, and postbiotics in humans remain to be established.
Also, it is indirect evidence of "cancer is an adaptation mechanism"
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 DEPTHCANCER Gut microbes shape response to cancer immunotherapy Science  03 Nov 20l                 Summary
  1. Jocelyn Kaiser
 See all authors and affiliations
This week, two studies offer a raft of evidence from cancer patients suggesting that the gut microbiome—the community of bacteria, viruses, and other bugs living in our digestive tracts—helps determine whether tumors shrink when treated with a powerful new type of cancer drug. Patients who took antibiotics for routine reasons before or soon after starting a type of immunotherapy known as a PD-1 inhibitor relapsed and died sooner than those who were antibiotic-free. And when mice received fecal transplants from patients who responded to the drugs, they did better on PD-1 blockers than did mice given nonresponder feces. Researchers are now planning a clinical trial to test whether manipulating the gut microbiome could help more cancer patients respond to PD-1 blockers.
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Accumulating evidence demonstrates that intestinal bacteria influence oncogenesis, tumor progression, and response to therapy. Thus, selectively manipulating the gut microbiota may represent a feasible means to (i) limit the incidence of specific tumors in the general population and/or (ii) improve the activity of various anticancer agents . Although the first possibility has been investigated in several models of oncogenesis with promising results, the actual oncopreventive effects of anti-, pre-, pro-, and postbiotics in humans remain to be established. Also, it is indirect evidence of "cancer is an adaptation mechanism"
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78 year lady underwent upfront lap sigmoid colectomy for a bulky tumor. Distal resection margin below promontory with distal resection margin 6 cm. post operative course uneventful. Final histology t3n1 with 2/30 nodes positive. However distal resection margin showed acellular mucin. Would she require resurgent for this or close observation with adjuvant chemotherapy?
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Patient recieved adjuvant chemotherapy and is on surveillance more than 2 years, disease free. No rerescection required
she underwent flexible sigmoidoscopy every 6 months
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Hi all,
I'm currently working on my Honours thesis was wondering if anyone has any literature or data in regards to combining the following chemotherapeutic drugs with Wnt inhibitors, preferably in colon/colorectal cancer (but other cancers are ok).
The panel of drugs I'm working on are:
Chemotherapeutic Drugs
- 5-fluorouracil (5-FU)
- irinotecan
- oxaliplatin
Wnt Inhibitors
- ICG001
- NSC668036
- PNU74654
- XAV939
Much thanks,
Thomas
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I think the following information helps you:
Tankyrase 1 inhibitior XAV939 increases chemosensitivity in colon cancer cell lines via inhibition of the Wnt signaling pathway as was written by Professor Xueyun Zhong (gdqylkp@163.com gdqylkp@163.com). Hans Clevers writes about the consequences of Wnt deregulation in colorectal cancer (clevers@niob.knaw.nl clevers@niob.knaw.nl)
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Is there any database for gut microbiota of colorectal cancer patients? Kindly help me in this regard. Where do I get the information of abundant value regarding the gut bacterial composition of colorectal cancer patients?
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Thank you Dr. Robert, Dr. Ahmed and Dr. Brunno for the information.
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I'm working on a multiplex IHC for analysing the TME in colorectal cancer focusing on potential beneficial versus detrimental immune infiltrates.
In that context I want to look at the macrophage polarisation (M1/M2-ratios). 
Will it be "sufficient" to double-stain only one of the macrophage populations? Planning on using CD163/CD206 for M2 and reasoning the rest of CD68+cells are M1, knowing that CD68 is a rather broad marker (also expressed by some DCs?). Alternatively, CD68/pSTAT1 for M1. 
Are there anyone having experience with these markers?
Grateful for response on this tricky subject!
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YOu did not mention that you are working with murine or human macrophages. Human macrophages are very different from murine macrophages. Human M2 macrophages dnt express CD163. Human unpolarized, M1 and M2 cells expression CD206. In human, CD163 was only expressed when cells are stimulated with IL-10. IL-4-treated human M2s dnt express Cd163. You check this ref: PMID: 25870903
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I have a young female patient with a rectal mass 3cm from anal verge. Biopsy has been done twice and both times showed only high grade dysplasia. MRI shows it to be a T3 lesion. No lymph nodes. Should she be started on neoadj therapy?? 
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Discuss it in a multidisciplinary committee, it is a question that involves considering many details
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Hi!
I am testing a new compound on colorectal cancer cell lines and I want to compare it's efficacy with the standard drug utilized in the treatment, which is the 5-FU. What concentrations should I use? I am using plasmatic concentrations found in blood samples collected from patients in treatment 2-3 hours after the infusion, are those concentrations considered clinically relevant? 
Thanks in advance.
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I  think to IC50  you can use in experiment
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I try to find out something relevant with the new clinical and experimental studies.
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Someone may be interested reading carefully the commentary written commentary by Dr. Stuart G. Baker, National Cancer Institute, Bethesda, MD, USA, which was brought up by Ijaz:
The questionable premises underlying the search for cancer driver mutations and cancer susceptibility genes.”
Dr. Stuart G. Baker, National Cancer Institute, Bethesda, MD, USA
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28 year male with signet ring low rectal cancer , cancer is suitable for intersphincteric resection on  MRI should we do isr or recommend aper
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I woluld not perform intersphincteric resection in signet-ring or poorly differentiated  cancer since there is too high a risk of local recurrence. What is more, the preoperative radiation or chemoradiation should be applied to improve local control after curative surgery.
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A case of a 57 year old patient, male, with a transvers colonic adenocarcinoma, moderate differentiated, tubular and small area of micropapillary carcinoma.
Thank you
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Looking at The Human Protein Atlas (proteintlas.org) p53 is mainly located in the nucleoplasm. Some of the cancer TMA´s for p53 in the human protein atlas show some accentuation of p53 staining in the nucleolus. 
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would you recommend adjuvant chemotherapy for t1 t2 no colon cancer with poor prognostic factors eg poorly differentiated or lymphovascukar invasion
any evidence for an against
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For IB colon cancer, pT2N0, no adjuvant treatment indicated. For stage Ii (pT3-4), only if high risk features after discussion with the patients.
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