The group held conference calls on Jan 13, Feb 24, April 21, and June 9.
Jan. 13: Dr. Merrell has accepted a new job and will become the Director of the School of Animal and Comparative Biomedical Sciences at the University of Arizona. Dr. Merrell will have 35 faculty in the School he directs. He will leave his position at USUHS at a date to be determined in March. Dr. Merrell has not yet decided about whether he will start a lab in his new position. Dr. Angela Melton-Celsa will take over Dr. Merrell’s grants at USU and she will maintain the PMP tissue samples until he decides about starting a lab in the new location. Dr. Angela Melton-Celsa needs to be added to the Mercy IRB protocol and MTA agreement so that PMP specimens can continue to be sent to USUHS. Ms. King said that the additions should not be difficult. Dr. Metcalf indicated that she has a Zoom account and can take over scheduling conference calls for the group. Everyone congratulated Dr. Merrell on his new position and wished him success in this new endeavor.
Dr. Li continues to work on a manuscript on his research with Dr. Testerman that involves isolating functional metabolites from PMP bacterial strains that Dr. Testerman cultured. He has carried out additional experiments to be added to the manuscript that was previously discussed. These experiments involved modifying the bacteria that he is studying. He will then study the properties of these altered compounds in terms of their effect on tumor cell lines.
Dr. Metcalf discussed the manuscript that she and Ms. Nieciecki are preparing on their microbiome work on PMP samples. They plan to move ahead with a paper that does not include imaging in it. A discussion took place about which journals to submit the paper to; mBio, a journal of the American Society of Microbiology (ASM), looks like a good choice. Another ASM journal, mSystems, is also a possibility. Dr. Metcalf plans to have the paper ready for submission within the next month.
Ms. King reported on the status of work at Mercy. Ms. Pawlikowski has taken over the fecal microbiome project and she is looking into completing the paperwork for submission of the fecal specimens. Hopefully the specimens can be sent to San Diego in the near future.
Feb. 24: Dr. Li discussed several points associated with his research. First, he has contacted the patent office at the University of South Carolina about patenting the compounds he has isolated from Dr. Testerman’s cell cultures. Dr. Li mentioned that naturally occurring compounds cannot be patented, but derivatives of them potentially can be patented. Dr. Li has discussed patent issues associated with publishing his manuscript with the university’s patent office. This office is checking with a patent attorney about how to proceed with patenting Dr. Li’s invention. Second, Dr. Li reported that he continues to work on writing up his manuscript. Finally, the material transfer agreement between the university and Mercy Medical is in place so tumor samples can be sent to Dr. Li.
Ms. Nieciecki discussed the status of the paper that she and Dr. Metcalf are writing up. There are two sections at the end of the paper that need to be finished. In the next two weeks Ms. Nieciecki should have some time to be able to complete these two sections. Then she can send the paper to the group for comments.
Ms. King reported on the status of work at Mercy. The MTA agreement between the University of South Carolina and Mercy has been completed and adding Dr. Angela Melton-Celsa to the MTA from USUHS is in the works. Dr. Melton-Celsa will be taking over Dr. Merrell’s lab when he leaves for his new position at the University of Arizona.
April 21: Dr. Li discussed several points associated with the manuscript that he is writing up. He mentioned that the tumor samples he has studied have additional bacteria in them compared to the new bacteria he is studying. Dr. Li wants to be careful before publishing his results. The new bacterial strain was isolated from a PMP tumor sample in Dr. Testerman’s lab and Dr. Li’s lab sequenced its whole genome using this isolate. However, Dr. Li wants to further confirm two points. First, if this strain indeed can invade PMP tumor cells. Previous confocal imaging showed that a few bacterial cells of this strain were present inside of PMP tumor cells. However, only a very few such bacterial cells inside the PMP tumor cells were observed. Thus, Dr. Li plans to use electron microscopy which has better resolution compared to the confocal imaging he used to confirm the invasion of this new species into PMP tumor cells. Second, how prevalent this strain is present in PMP tumor samples. The Metcalf lab kindly offered to check if they saw the presence of the 16s gene of this strain in their PMP bacterial metagenomic sequences of different PMP tumor samples.
Ms. Nieciecki discussed the status of the paper that she and Dr. Metcalf are writing up. There are two sections at the end of the paper that need to be finished. In the next two weeks Ms. Nieciecki should have some time to be able to complete these two sections. Then she can send the paper to the group for comments. Ms. Nieciecki also discussed results that she has gotten from studying the microbiome of canine tumors. Similar to the PMP tumors she has found a lot of off-target DNA amplification. She also has found considerable microbial diversity in the canine tumors. Ms. Nieciecki mentioned that within tumor diversity could result from spatial differences in pH and oxygenation. Ms. Nieciecki mentioned that some of the bacteria in PMP tumors may be associated with stays in hospitals. Finally, Ms. Nieciecki mentioned a recent paper that discussed tumor-resident intracellular microbiota that promote metastatic colonization in breast cancer. After the call she emailed the following link to the paper: https://pubmed.ncbi.nlm.nih.gov/35395179/
Ms. King reported that Mercy has fully executed the material transfer agreement (MTA) and protocol amendment with Dr. Melton-Celsa and USUHS. They plan to send a big batch of samples next week. Mercy has also reached out to Dr. Li about sending samples, but he is not quite set up yet to start receiving new ones so they are waiting for him to resume sending samples. Mercy has started looking at the fecal microbiome samples, but haven’t made much progress. It is proving tedious to ensure that all 3 kit barcodes are registered to the same individual and whether or not they completed the required questionnaires at all 3 collection points.
The group held a conference calls on June 9, July 21, Sept. 15, Oct. 27, and Dec. 15. The next conference call is scheduled for Feb. 9, 2024.
June 9: Dr. Li discussed two points associated with the manuscript that he is writing up, since he wants to be careful before publishing his results. First, the new Streptomyces strain he is studying was isolated from a PMP tumor sample in Dr. Testerman’s lab. Previous confocal imaging showed that only a few bacterial cells of this Streptomyces strain were present inside of PMP tumor cells. As an additional follow up Dr. Li plans to repeat the co-culturing experiments to hopefully consistently observe the invasion of the Streptomyces strain into the PMP tumor cells. Dr. Li again pointed out that he has not seen any report regarding Streptomyces invading tumor cells. After the co-culturing experiments of the Streptomyces strain and the PMP tumor cells are repeated, confocal imaging will again be used to detect the bacterium.
The second issue involved how prevalent Streptomyces is present in PMP tumor samples. The Metcalf lab kindly offered to check if they saw the presence of the Streptomyces strain found by Dr. Li in their PMP bacterial metagenomic sequences from different PMP tumor samples. They found other Streptomyces sequences that were different from the strain found by Dr. Li. Ms. Nieciecki looked for other Streptomyces sequences and found 5 different amplicon sequencing variants. These were found in 4 different PMP tumor samples at very low abundance (9-29 reads per sample). One of these ASVs was actually found in both replicates of a PMP sample that was extracted and sequenced in both labs which is promising.
July 21. There were no new developments to report from the July 21 conference call.
Sept. 15: Dr. Li discussed his research on the new Streptomyces species which appears to invade tumor cells. Dr. McAvoy mentioned his initial work with Dr. Dubois on H. pylori in 2004. When 10 PMP tumor specimens were tested by a pathologist at St. Agnes Hospital, all tested negative for H. pylori. However, when Dr. Dubois’ assistant Dr. Semino-Mora subsequently tested three PMP tumors two tested positive for intracellular H. pylori. Figure 3C in Dr. Semino-Mora el al’s 2008 paper in Annals of Surgical Oncology shows H. pylori inside a goblet cell. This paper is available in the Publications section on this site. A discussion was held about whether intracellular bacteria could hide from the immune and whether they might be a cause of PMP. Dr. Testerman stated that she felt that more important than whether bacteria were intra- or extra-cellular was the products put out by the bacteria in terms of causing cancer. Dr. Li also discussed how he is approaching the claim of a new Streptomyces species. He has been in contact with someone in Oklahoma in connection with this effort.
A discussion of the draft of the manuscript that Ms. Nieciecki emailed to the group took place. Everyone praised Ms. Nieciecki for the high quality of the manuscript. Dr. Metcalf said a last call for any changes would be sent to the group, after which the manuscript would be submitted. Dr. McAvoy raised the question of whether there might be a way of sharpening conclusions from our microbiome work, for example by looking at bacteria that are known to upregulate MUC2 production. A discussion about his question took place.
Oct. 27: Dr. Li discussed two points about his research. First, regarding a unique Streptomyces species that Testerman’s lab previously isolated from a PMP patient tumor sample, his previous analysis comparing its genome with other available Streptomyces genomes suggested that this species is likely a new Streptomyces species. To further confirm this, Dr. Testerman connected him with a microbe identification expert from University of Oklahoma and he sent him his data and is waiting for his analysis for confirmation. Second, the PMP cell lines that Dr. Testerman’s lab established from patients’ primary tumors could be repeatedly passaged and thus provided us with a unique opportunity to screen for lead compounds against PMP. Using our geographically and phylogenetically diverse in-house microbial library featuring several hundred bacterial strains, we discovered a novel class of compounds we named which exhibited an activity against PMP cell lines comparable to the anticancer drug mitomycin C. Notably, these compounds did not exhibit cytotoxicity to three normal cell lines that were exposed.
Dr. Metcalf reported that not a lot had been done since our last conference call. An issue that arose with the submission of our latest manuscript involves a controversy that has arisen with an earlier microbiome paper on which Dr. Metcalf was a co-author. A rebuttal to that paper was sent in, and Dr. Metcalf’s co-authors replied to the rebuttal. Although our current paper does not contain significant material related to the controversy, Dr. Metcalf felt it would be wise to delay its submission somewhat. In the final paper Dr. Metcalf said that a sentence on the controversy will probably be added at the end of the paper. A discussion took place about which journal the latest paper should be submitted to. mSphere appears to be a good choice. Ms. Nieciecki raised the issue of whether the nomenclature on PMP in the introduction of the paper should be updated. It was suggested that Dr. Sardi could be asked about this point. Dr. Metcalf mentioned that we discuss different types of PMP in the introduction, but then do not discuss this point after that. A brief discussion should probably be added at the end of the paper.
Ms. King reported that at a recent conference, Peritoneal Surface Oncology Group International 13th PSOGI International Congress on Peritoneal Surface Malignancies, our microbiome research was cited in oral plenary presentations discussing how there hasn’t been much work in determining causes of appendix cancer (except for us) and possibly using the microbiome as a way to help clarify the classification/differentiate between DPAM/PMCA/PMCA-S etc. Given all the other work that she and Ms. Pawlikowski has been involved with, progress on finalizing the fecal microbiome specimens for submission has been slow. Paper work needs to be completed.
Dec. 15: Dr. Li discussed several points about his very innovative research on PMP. He used a powerpoint presentation to illustrate these points. He has isolated several compounds from PMP cultures and they have good properties in terms of apoptosis in PMP tumor cells. They also do not show toxicity to normal cells. Dr. Merrell suggested trying to test the compounds using appendiceal cell lines. Dr. Testerman suggested contacting NCI since they have cancer test panels that potentially could be used.