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
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.
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):
- AdvDMEM+++ (see recipe)
- 1× B-27 Supplement
- 20% (v/v) Rspo1-CM
- 100 ng Noggin
- 1.25 mM N-acetylcysteine
- 10 mM nicotinamide
- 10 μM p38 inhibitor SB202190
- 50 ng/ml epidermal growth factor
- 0.5 μM ALK5 inhibitor A83-01
- 1 μM prostaglandin E2
1. Cultrex BME (R&D)
TrypLE + Rhoki
Refresh medium every 2-3 days
Passage every 7 days.
Each taken gene ontology for dysregulated genes set in colorectal cancer has a biological function in neurogenesis. Can anyone explain why?
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.
After low or ultralow anterior resection, it is difficult to assess the future bowel function before reversing the ileostomy
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
I am analysing data for colorectal cancer study
Among the data
I have 3 columns
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??
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?
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.
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!
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?
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).
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.
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!
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!
"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 . 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.
Chapter Chronic Inflammation
"Chronic inflammation can result from the following:
- 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.
- 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.
- 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).
- 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.
- 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 1 beta
Tumor Necrosis Factor - alpha
If CRC patients had a hair sample analyzed for fungal cultures, what fungi would be found?
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.
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.
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?
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.
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?
"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
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?
- "Intestinal microbiota and colorectal cancer: a new aspect of research" https://www.ncbi.nlm.nih.gov/pubmed/30512251
(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?
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.
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 ?
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,
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!
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?
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.
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.
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.
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?
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?
How do you approach circumferential suspicious Polypoidal mid Rectal lesion which yield high grade dysplasia by 2 different senior endoscopist?
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?
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 ?
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.
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.
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
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!
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?
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
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?
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
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 !
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.
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!
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.
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?
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.
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)
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??
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?
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"
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"
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?
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:
- 5-fluorouracil (5-FU)
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?
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!
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??
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.
28 year male with signet ring low rectal cancer , cancer is suitable for intersphincteric resection on MRI should we do isr or recommend aper
A case of a 57 year old patient, male, with a transvers colonic adenocarcinoma, moderate differentiated, tubular and small area of micropapillary carcinoma.
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