 Welcome to MOOC course on Introduction to Proteogenomics. In the last lecture, we had invited clinician scientist Dr. Sachin Jadhav, who gave you very broad clinical perspective and thought provoking points about how various type of clinical requirements can now be met using the OMEC data sciences. However, there is still lot of gap and there is a need for good collaboration. So, today's lecture Dr. Jadhav will talk to us about the proteogenomics in hematology and BMT and how it is going to impact the patient care. We will also talk about the treatment planning of a patient based on the nutritional profiling. We will further illustrate how tailored therapy for the patients are required and reason why it could not be resolved or achieved even till date. So, let us welcome Dr. Sachin Jadhav for his talk on clinical considerations for OMEX and how it could be helpful in treating diseases effectively. Rational drug design. The tyrosine kinase which is constitutively activated, no, it is a pathogenic mutation. It is the first pathogenic mutation that was identified, phyletalphae chromosome, translocation 922. So, this mutation gives rise to an abnormal tyrosine kinase which is constantly active and hence the cells multiply and hence leukemia happens in those patients, right. So, now this is the abnormal tyrosine kinase and it has a certain pocket and it was thought that if we can create a small molecule which will go and sit there, then this tyrosine kinase will not be able to work. So, this is called as rational drug development, rational drug designing. Until this point all the medicines in our life from chloroquine for malaria, penicillin for you know as an antibiotic or chemotherapy were found by accident, were found by accident. Most of the scientific discoveries are by accident, right. People would try 100 things and something kills the cell, ok, let us use this. This is where first time rational drug design because now you know the pathobiology and you know maybe if I can create something that in coin inhibited, right. The first time this was done glyvec that is imatinib was created and it changed the world for CML patients. All of these patients with chronic myeloid leukemia, all for cure they had to undergo bone marrow transplant. They had to that was the only known treatment or the best treatment. They were other treatments, but not good enough. After this medicine came this is one tablet, it is one tablet per day. This medicine turned CML, chronic myeloid leukemia, the treatment became as simple as a treatment of diabetes. You just take one tablet a day. You take one tablet a day and you can see the overall survival at 80 almost 70 percent overall survival at 5 years. No bone marrow transplant just one tablet because now this tablet goes and attacks that abnormal tyrosine kinase and this is the targeted therapy that you mentioned, right. So, this is where now we are getting into rational therapy and then people started thinking well let us find more mutations, more targeted therapy, let us make life easy until this happened. We started doing genomics and acute myeloid leukemia, acute lymphoblastic leukemia and this is the current mutational profile of AML patients. So, if you take a thousand patients with acute myeloid leukemia and look for mutations you will get NPM, CBPA, TP53, you know DNMT everything, every patient will have one or two mutations and we really do not know, we do not know what to do with these and then you have to follow them for 5 years. And then you understand well if this subset with mutations they have better prognosis those have bad prognosis and then you think those who have bad prognosis chemotherapy is not going to work, we have to do a bone marrow transplant etcetera, etcetera. But genomics has thrown so much information that we cannot deal with it. We do not know how to use this rationally to practice in a sensible manner. So, we have some guidelines now remember these are non-pathogenic mutations these are just discovered they are not necessarily driver mutations they are just discovered, but they affect the behavior of the cancer. Some mutations will worsen the outcome others will make it better. So, whichever mutations make it better great favorable risk just give chemotherapy bone marrow transplantation not required. Those who have bad mutations you have to do bone marrow transplantation etcetera So, that is how we are using this information currently right. So, diagnose a leukemia if there is a target able mutation like TML rara or BCR ABL that is Philadelphia treat with targeted therapy. There is no target able mutation give some chemo look at the mutational profile at the end of the first month. If that person has some good mutations give further chemo and stop if by chance that person does not have good mutations then chemotherapy is not going to cure you need to do a bone marrow transplant correct. So, that is how what we are doing, but then this is blind therapy to some extent it is better than what we were doing even 5 years ago because now at least we have some mutations which are guiding us, but it is largely blind right. And in this current risk stratification about 30 40 percent of patients unnecessarily get a bone marrow transplant that is the limitation of our understanding today we are not able to perfectly risk stratify patients and give perfectly tailored therapy it was supposed you know 5 years ago we were supposed to have tailored therapy for everybody it really has not happened. And we end up recommending transplant to 50 60 percent of acute malar leukemias and you know what is the biggest side effect of a bone marrow transplant GVHD graft versus host disease anything else rejection blood group changes sure if the patient and donor have different blood groups anything else we get because even 50 percent matches today we are getting good results almost everybody has a donor nowadays biggest side effect of bone marrow transplant there will be no compromise they get infections some patients die of infections about 20 percent of our patients die of infection what else financial toxicity financial toxicity and that is why this is a problem. So, we need you guys to do a better job so that we do not do this we depend on you guys to tell us how to better categorize cancers how to treat what not to treat what to do what not to do because ultimately we are delivering health care based on what you publish and it is not only this, but like you said there is a lot of morbidity so 60 percent of our patients after transplant do well 20 percent will die of chemotherapy of complications 20 percent more will survive with bad complications and I will show you a patient right and one of this is one of the worst complications if the patient is surviving surviving with graft versus host disease in about 5 percent of patients is they need a miserable life they are alive, but it is not a good life right. So, we do an allogenic stem cell transplant allogenic means we take a donor we put the donors stem cells into the recipient before that we give chemotherapy and kill off the recipients native marrow and then you put in the donor stem cells the donor stem cells go in and they engraft they create a new marrow as they create a new marrow the donor cells may attack the host and cause graft versus host disease GVHD this GVHD will happen in the first 100 days in 30 percent and 10 percent will die because of it right. Now, this is so bad in spite of the best immunosuppression patients will die so we need a rapid diagnostic marker if we wait until clinical symptoms develop it is already too late we need a serological marker which we can track right it is like checking for temperature until the patient becomes septic we need a serological protein marker which we can track before there are symptoms of GVHD because after that 10 percent die no matter what you do how much ever money they have because when this happens families tell us doctor I will bring as much money as is required do everything you can be anybody in this world if you have bad GVHD you are going to die there is no medicine in this world which can stop you if you survive 30 percent will get chronic GVHD that means they will have long term problems and for these again 10 percent of them will have long term morbidity they cannot go to work they cannot go to school they cannot play with their friends children cannot play with their friends etcetera they are restricted because of chronic GVHD. So, this needs prognostic marker to monitor therapy we are giving treatment, but we have to look at the patient after 3 months we need something which can give us an early indicator of response to treatment. So, you see the gaps in our knowledge you see how much work has to be done. So, how can we go ahead we need to understand graft versus host disease is an immunologic disease it is the donor cells immunity the new immunity attacking the host from inside is the new immunity is a new police which are supposed to help, but the police are attacking civilians right. We try to do HLA matching like you said so, that we decrease the risk of GVHD we ensure that the patient and donor are as well matched as is possible, but still it does not really protect everyone and there is absolutely no genomic marker which can help us predict that yes this patient is at a higher risk or this donor recipient pair is at a higher risk of GVHD there is no genomic marker. Late diagnosis like I said leads to mortality. So, we have to find something by which by way of by means of which we can do an early diagnosis right and predict resistant to conventional treatment. Currently we give medicines and we have to wait for 3 days in those 3 days if the person is not responding he is gone we need some early predictive marker for response to treatment right. Acute GVHD is a systemic disease skin is affected, gut is affected, liver is affected there is widespread tissue injury and hence plasma proteins can be looked at. Maybe in the blood we will find some markers because this is a widespread systemic disease the entire body is practically affected acute GVHD. Chronic GVHD is localized dry mouth dry eyes skin lesions. So, we can look at the tears for a proteomic profile because these is a localized disease right and hence tissue fluid tears saliva because the GVHD is localized to that part of the body it is not generalized tissue fluid needs to be analyzed. There is some work which has been going on for over 10 years now for over 10 years and many people are claiming well we have a panel which can predict etcetera etcetera work is still going on this is one of this I am just giving you a flavor of what is happening in the world. This can also help us provide a therapeutic guidance. So, for example, proteomics has shown that soluble ST2 receptor is elevated in chronic GVHD. So, if you can create an inhibitory drug maybe it will help and it has shown in this study which was conducted on a mouse model recently reported in I think July this year in JCI. So, maybe if we do good work we can figure out some treatment you know policies strategies etcetera and this if in this paper at least in this study when they created an inhibitor to soluble ST2 receptor it decreased GVHD in the mouse model. Same thing chronic GVHD ocular tear film was looked at and some normal proteins were identified this is a review of various proteins which have been identified to be up regulator or down regulated, but you can see really nothing that is clinically relevant today. So, much more work needs to be done maybe if something is clinically relevant we can target it with some targeted molecule targeted medicine, but well we have to see maybe what we can do in the future and hopefully the near future because we are transplanting patients. We are currently transplanting patients who need this today, but at least maybe in the near future what we can do is we can look at the blood biomarker before clinical symptoms come up in the early stage and if that person's blood biomarker stays negative we can decrease immunosuppression rapidly. We have to give immunosuppression to transplant patients so that they do not have rejection in GVHD, but that leads to infection. So, we can decrease immunosuppression rapidly so that they do not get side effects of medicine. However, if they seem to be at a high risk because the biomarker is going up then we will we may actually intensify immunosuppression and prevent GVHD if we can find a biomarker. I will just show you two patients and then I end this is the impact which could have been created this is a boy he is now do you have you seen you have not seen. So, this is a boy from North Karnataka I think he is now 10 years old he came to us with acute myeloid leukemia. We did a pre-emptive transplanting that is because he had an MLL mutation. So, acute myeloid leukemia with MLL mutation is bad you need to transplant. So, we transplanted him he went through lot of complications and now this is chronic GVHD this is his skin those are his legs it is not bad he did manage to go to Thailand with his family, but he is he is not normal he cannot go to school he cannot play with his friends because he is on a immunosuppression and he can any time pick an infection he is on so much steroids that he can pick TB for all we know because his immunity is suppressed by our medicines and these medicines were given to treat GVHD and they can have a side effect of immune suppression. So, we need to do better in this that is another patient she is from Sri Lanka and again MLL she had intermediate risk. So, not really bad high risk, but intermediate risk and we felt it was best to again treat her with a prophylactic transplant before she gets a disease relapse because she still has intermediate not good risk. She has some minor lung GVHD. So, she has some cough and phlegm, but not bad very active works in a bank in Sri Lanka leading a near normal life, but then what about the financial toxicity they had to borrow money. So, if we could have a better understanding of whom to transplant and whom not to transplant maybe we should not have transplanted right that is our team right those are the doctors and then you have the nurses and that is the administrative team we have clinical pharmacists everybody working together those that is the nurse educator BMT coordinator etcetera, etcetera. But what about this? Thank you GVHD. So, 40 percent of patients will develop GVHD I mean it is between 30 to 50 percent in different series let us say 40 percent will develop now this 40 percent 10 to 15 percent will die because of this. We are able to avoid 60 percent from getting GVHD, but 40 will still get it does not help because there are many more minor antigens we are matching 10 HLA antigens HLA, A, B, C, DR, DQ and now DP as well. So, 12 HLA antigens right, but there are lots of minor antigens which are different and it still causes. So, the reason GVHD developed is much it is different before transplant we have to give chemotherapy. Chemotherapy causes tissue injury and reveals new antigens and the upcoming new donor cells in the body will look at these new antigens and then neo antigens and mount a immune response. So, it is not just the HLA, but various other antigens which are different between the recipient and the donor. Step 1 good idea let us do it no problem that is called as an autologous transplant autologous your own stem cells and that is done that is done in some patients there are reasons why we do autologous transplants in some and allogenic in others. The reason we do allogenic transplant that means you take another normal human being his or hers stem cells and inject into the patient is you are trying to create a new immunity. One of the concepts of cancer is it is a failure of immune surveillance is that right malignancy is a failure of immune surveillance. So, this is a patient who had has bad cancer his own immunity failed to prevent it and it is so bad that if it comes back it again cannot fight this is a terrorist I mean cancer is like a terrorist correct immunity is like the police if while we are sitting here imagine after this talk you opened your phone and you saw that 5000 terrorists were discovered in Mumbai. The first thing that you will think is what were the police doing? How did 5000 terrorists come in and even if we kill these terrorists what is the guarantee that this police will not be able to stop the next attack because these fellows are useless. So, there are some cancers that is what I said high risk for relapse where you are scared that this person's immunity cannot fight the cancer if it relapses that is where you change the immunity by giving somebody else's stem cells and thus new RBC's new WBC's new platelets and new WBC's means new police. So, rejection today in today's transplant practice is less than 5 percent because we have good HLA matching less than 5 percent risk of rejection. No for about anywhere between 9 to 12 months after that we take them off immunosuppression they go back to normal life one of our patients was a BSF soldier we took him off immunosuppression here to go back to the border and he said I do not want to go back to the border. So, they lead a healthy I mean 60 percent of patients lead a healthy normal life fantastic question. So, that can be done and we do that. So, we use a medicine called cyclophosphamide which is given on day 3 day 4 of transplant to cut off the alloreactive T cell population which is coming up on day 3 4. T cells can also be reduced by putting some other medicines in the stem cell bag or given them as injections, but they do not uniformly help and when you are cutting the T cells you may also be killing the good T cells which will give immunity to the recipient. So, it is not yet a perfect science, but that is a very good question. So, that is another form of immunotherapy allogenic BMT is immunotherapy because you are changing the immunity that is another form of immunotherapy where either you use dendritic cells or you use what is called as CAR T cells, chimeric antigen receptor T cells. It is USFD approved for certain cancers, but we have to look at the long term. So, less than 50 patients in the world have received it and currently one patients therapy costs 3 crore rupees yeah you cannot do anything. So, chemotherapy is like carpet bombing yeah. Like I said there are 5000 terrorists were found in Mumbai get a plane from a drop a bomb terrorists may die normal people will die. So, cancer cells will die normal bone marrow will die in all of our patients the bone marrow actually gets completely killed. So, WBCs go down to 0 late let us go down to 0 there is no way as of now we do not know. In conclusions today you have learned why there is an urgent need of a proper classification of disease like leukemia or in fact it is true for any cancer type. Many diseases like leukemia which required organ transplant mostly leads to the drafts versus whole disease also known as GVHD blood group even may change and many their immune system based complications. Those rare number of patients which live longer than most others they live diseased and painful life. In India these cases are also economically toxic as most of the Indian population cannot afford these kind of treatments. We also heard the need of early diagnosis of GVHD conditions in such diseases. Also we learnt about how proteomics genomics or proteogenomics could help clinicians and patients to find diseases like leukemia better and effectively. The next lecture is going to again shift gates bring back the proteogenomics how to integrate genomics and proteomics information and utilize the combined power of proteogenomics for various diseases especially in context of cancer and we will have another invited speaker Dr. David Fanio who will deliver the talk. Thank you.