Biotech Research Club hosts a series featuring current graduate and post-graduate students sharing their work. The sessions are followed by informal discussions about academia, getting into graduate school and more! Get in touch with us if you’d like to present your work!
Upcoming Talks
This week’s edition of our Alumni Talks Series features Atmika Paul, who did her MS from IITM and is currently pursuing a PhD at the Max Planck Institute.
Title: Deciphering the role of TGF-ß signalling in maintenance of genomic integrity in pancreatic cancer
Date and Time: Friday, 9th April, 2021 at 8:30 PM
Link: meet.google.com/krw-wkhx-xra
Query form: https://cutt.ly/5cC1ctq
Biography of the speaker: She did her Master’s in research in cancer biology in Dr. Mahalingam’s lab, and later joined as a PhD research scholar in NUS Singapore. Then she finished her Master’s/PhD coursework with the International Max Planck Molecular Biology program and currently she is pursuing PhD in Cellular Oncology. She is also the student representative of the Pancreatic cancer Genome dynamics research unit. She works on understanding the underlying molecular mechanisms that govern cancer progression and define targeted therapeutic strategies for better clinical management of cancer.
Abstract: Clinical management of Pancreatic Cancer (PC) continues to be a formidable challenge despite recent breakthroughs in diagnostics & therapeutics. Pronounced Chromosomal Instability (CIN) is a hallmark of PC and is associated with therapeutic resistance, increased metastasis, late-stage diagnosis and poor 5-year survival rate (~5-10%), making it one of the most lethal cancers. Alarmingly, it is predicted to become the second-leading cause of cancer-related deaths by 2030. Although pathologically heterogeneous, the PC genome shows recurrent patterns of genetic alterations. Thus, combining molecular-driven therapeutic approaches with current histopathological criteria can significantly improve patient stratification.
One of the most frequent genetic alterations in Pancreatic Ductal Adenocarcinomas (PDACs) is the inactivation of SMAD4 (~55%), a central mediator of canonical TGF-β signaling pathway. Our recent work suggests that altered TGF-β signaling directly affects CIN in PDACs. Mechanistically, we found evidence that these chromosomal aberrations are driven by abnormal microtubule dynamics in mitotic cells. Our project aims at dissecting the molecular consequences of aberrant TGF-β signaling in pathogenesis of PC. This research will improve understanding of pathways governing genome maintenance and explore exciting avenues for stratifying SMAD4-deficient PC patients. We hope to devise a novel strategy for targeting pancreatic cancer by combining existing microtubule-targeting drugs and anti-TGFβ therapies.
Old Talks
This week’s edition of our Alumni Talks Series features Dr. Dhruva Katrekar, an alumnus of the Batch of 2015, who just completed his PhD from UCSD.
Title: Engineering a programmable RNA editing toolset for in vivo gene therapy
Date and Time: Friday, 26th March, 2021 at 8:00 PM
Link: https://meet.google.com/gmi-qtyo-qbq
Query form: https://cutt.ly/UxDZb9E
Biography of the speaker: Dhruva Katrekar graduated with a B.Tech in Biotechnology from IIT Madras in 2015. While at insti, he worked with Dr. Madhulika Dixit in the Vascular Biology Lab studying endothelial dysfunction in type II diabetes. He also spent the summer of 2014 at the IGBMC, France, studying development of heart valves in zebrafish embryos, via the Charpak Internship Program. From these experiences he was convinced of pursuing graduate school and believed that he would continue working in the cardiovascular biology space. He then started graduate school at UCSD in 2015 and on being exposed to their cutting-edge research, he was quite fascinated by the field of gene therapy that was blossoming with the advent of the CRISPR-Cas system. Thus, in his second rotation, he decided to try Dr. Prashant Mali’s research group which was focused on building new tools for gene therapy and this is where he ended up spending the last 5 years. During his PhD, he worked on developing various tools such as a programmable adeno associated virus for gene delivery, a split-Cas9 for in vivo gene regulation and an adenosine deaminase based RNA editing tool for correction of point mutations in vivo. He graduated with a PhD in Bioengineering in January 2021 and is looking to spend the next couple of years trying to enable clinical translation of the RNA editing toolset. He believes that technology development is a highly risky space but allows one to unleash one’s creativity!
Abstract: While human genetic diseases can be caused by point mutations, insertions/deletions, chromosomal translocations or copy number variations, point mutations account for 58% of the pathogenic genetic variants causing disease. Programmable nucleases such as CRISPR-Cas are powerful tools but their use for the correction of point mutations in vivo poses some major challenges, namely, the threat of introducing permanent off-target mutations in the genome and immunogenicity due to their prokaryotic origin. In this talk, I shall discuss development and characterization of an RNA editing toolset of human origin for correction of guanosine-to-adenosine mutations and premature stop codons. I engineer guide RNA to recruit endogenous and exogenous human adenosine deaminase acting on RNA (ADAR) enzymes to target transcripts and catalyze adenosine-to-inosine (guanosine) modifications. In proof-of-concept studies, I repair disease-causing premature stop codons and splice-site mutations in mouse models of Duchenne muscular dystrophy (DMD), Hurler syndrome and ornithine transcarbamylase (OTC) deficiency.
This week’s edition of our Alumni Talks Series features Mr. Suresh Balsubramani, an alumnus (BTME-76), who is a corporate professional with significant interdisciplinary experiences in biology businesses.
Title: Career Opportunities in the Biotechnology Industry
Date and Time: Friday, 19th March, 2021 at 9:00 PM
Link: meet.google.com/mcg-kyqp-kpy
Biography of the speaker: Mr. Suresh Balsubramani is an alumnus of IIT Madras, graduating with a B.Tech degree in Chemical Engg in 1976. While he preferred Math to Biology in school, he has spent his entire career in Biology. He is a consummate corporate professional and has significant interdisciplinary experiences in plant health, animal health, and human health businesses. He has met customers personally in over 50 countries around the world.
Abstract: ‘The Age of Living Machines: How Biology Will Build the Next Technology Revolution’ is a book written in 2019 by Susan Hockfield, neuroscientist and past President of MIT. There is a biotechnology revolution beginning to happen that will define our lives the next 20+ years, in food, health, climate change, etc. The field is just taking off and what was unthinkable is beginning to happen. These developments provide significant industry opportunities for students with diverse skill sets. Students have an opportunity to reflect on the future and position themselves to leverage their unique knowledge, skills, and attitude. This talk will define possible opportunities in industry and help students to position themselves for a rich career ahead.
The Biotech Research Club is very happy to announce that this week’s edition of our Alumni Talks Series features Dr. Ganesh Kadamur, an alumnus of the Batch of 2008, who is currently a senior scientist at AstraZeneca.
Title: My journey from IITM to graduate school and onto pharma R&D
Date and Time: Thursday, 11th March, 2021 at 6:30 PM
Link: https://meet.google.com/qjh-jvsz-axv
Biography of the speaker : I did my BTech Biotech at IITM passing out in 2008. I then went on to do a PhD in Molecular Biophysics at UT Southwestern Medical Center, Dallas working on G protein signaling in the lab of Dr.Elliott Ross. After this, I was a NCBS-Cambridge postdoctoral fellow in the labs of Dr.Christian Frezza and Dr.Sunil Laxman, where I did various projects on understanding yeast metabolism, designing metabolite sensors and applying these to study metabolic rewiring in cancers. I then joined AstraZeneca as a senior scientist in the basic R&D division, where I am a member of the Discovery Sciences team working on different oncology projects.
Abstract: I will give a brief overview of the path I have taken so far that led me from insti to a career in research across academic and industry institutions. I will focus on the decisions and actions that created this path, and hope to share what I have learnt along the way.
The Biotech Research Club is very happy to announce that this week’s edition of our Alumni Talks Series features Dr. Poornima Kolhar, an alumnus of the Batch of 2006, who is currently a management consultant with product strategy experience at L.E.K.
Title: What I wish I knew when I was at insti!
Date and Time: Thursday, 25th February, 2021 at 9:30 PM
Link: https://meet.google.com/pfx-mkbz-jqk
Biography of the Speaker: Poornima Kolhar is from the first batch of Biotech at IITM. She graduated in 2006. After her Btech she did her PhD in Bioengineering from UCSB where she designed nanoparticles for better bioavailability. After her PhD, she worked at Theranos - arguably the most famous (or infamous) biotech company in the silicon valley. She then went on to get her MBA degree from INSEAD (France) and she is currently a management consultant at LEK consulting.
Abstract: After graduating from IITM, I have done a PhD, worked at a startup, got a business degree and am a business consultant. I will share 2-3 stories from my experience that hopefully will be useful to the students in their careers.
The Biotech Research Club is very happy to announce that this week’s edition of our Alumni Talks Series features Dr. Swathi Ayloo an alumnus of the Batch of 2010, who is currently doing a postdoc at Harvard Medical School.
Title: Intracellular communication regulating Blood-Brain Barrier Integrity
Date and Time: Friday, 29th January, 2021 at 7:30 PM
Link: https://meet.google.com/qpm-jrga-hcy
Biography of the Speaker:
Dr. Ayloo did her undergraduate degree at IIT Madras in the Dept. of Biotechnology and went on to do a Ph.D. at the University of Pennsylvania. Her research thesis was focused on understanding transport mechanisms at the single-molecule level as well as within cells. She also developed and implemented tools to optogenetically manipulate trafficking within neurons to better understand regulatory mechanisms of molecular transport in the nervous system. She is currently doing a postdoc at Harvard Medical School working at the interface of neuronal and vascular biology, focusing on the blood-brain barrier.
Abstract:
Blood-central nervous system (CNS) barriers are functional interfaces separating the neural tissue from circulating blood and are essential for neuronal function and cellular homeostasis. Endothelial cells forming the walls of the blood vessels make up these barriers. Barrier properties are not intrinsic to CNS endothelial cells, but rather, are induced by the underlying microenvironment of the tissue. The specific extrinsic factors from perivascular cells that regulate barrier formation are, however, largely unknown. Here, I present a brief overview of our current understanding of how perivascular cells induce barrier properties in the CNS and provide some of our current findings in this area.
This week’s edition features Shruthy Suresh Aggarwal, an alumnus of the Batch of 2013 who is currently a postdoctoral fellow in the Department of Cancer Biology & Genetics, Memorial Sloan Kettering Cancer Center.
Title: A CRISPR-Cas9 screen reveals novel mechanisms of PD-L1 regulation in human lung Cancer
Date and Time: Thursday, 21st January, at 6:30 PM
Link: meet.google.com/njj-nxzw-mra
Biography of the Speaker:
Dr. Shruthy Suresh Aggarwal was born and raised in Chennai for 21 years and received a B.Tech in Biotechnology from IIT Madras in 2013. During this time, she worked in Dr. Karungaran Devarajan’s lab in the Department of Biotechnology for her Bachelors thesis work. A summer of exciting research at Michigan State University as a Khorana Scholar in 2012 motivated her to pursue graduate studies in the US. She obtained her Ph.D in Cancer Biology from the University of Texas, Southwestern Medical Center as an HHMI Med to Grad fellow in 2019. Her Ph.D thesis work in Dr. Kathryn O’Donnell’s laboratory has focused on using CRISPR based screening to identify regulators of the PD-L1 immune checkpoint in lung cancer. Her work contributed to the lab being awarded several grants: Welch Foundation Grant 2018, Friends of the Comprehensive Cancer Center Award in Cancer Research 2017 and NCI SPORE in Lung Cancer Career Development Award 2016. Shruthy is currently a postdoctoral fellow in the Department of Cancer Biology & Genetics, Memorial Sloan Kettering Cancer Center. Her work on melanoma metastasis in Dr. Richard White’s lab is funded by a Melanoma Research Foundation Career Development Award and a Translational Research in Oncology Training award.
Abstract:
Cancer cells express high levels of PD-L1, a ligand of the PD-1 receptor on T cells, allowing tumors to directly suppress T cell activity. Monoclonal antibody-based checkpoint inhibitor blockade (CIB) therapeutics (including anti-PD1 and anti-CTL4 therapies alone or in combination) have revolutionized the treatment of non-small cell lung cancer (NSCLC) and are now used as front-line therapy. However, only ~20% of all NSCLCs benefit from checkpoint blockade. Therefore, it is imperative to understand the mechanisms regulating immune checkpoints in lung cancer. We used Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)- based screening to identify regulators of PD-L1 in human lung cancer cells. Uroporphyrinogen Decarboxylase (UROD), a key enzyme in the heme biosynthesis pathway, was identified as a potent PD-L1 negative regulator. We show that impairment of heme production, which activates the Integrated Stress Response (ISR), results in enhanced PD-L1 translation. PD-L1 translation is repressed by non-canonical upstream open reading frames in its 5’ UTR, which are bypassed by ISR pathway activation, leading to suppression of anti-tumor immunity. We demonstrate that ISR-dependent translation of PD-L1 requires the translation initiation factor EIF5B. EIF5B overexpression, which is observed in human lung cancers and associated with poor prognosis, is sufficient to induce PD-L1. These findings uncover a new mechanism of immune surveillance regulation and suggest novel targets for therapeutic intervention.
The Biotech Research Club is excited to host Srinivas Allanki, a final year PhD student working with Dr. Sven Reischauer and Prof. Didier Stainier at the Max Planck Institute for Heart and Lung Research in Germany. Using the highly regenerative zebrafish as a model system, he studies the fundamental mechanistic differences between regeneration, and forming a permanent and functionally inert scar after tissue damage. He is an alumnus of the dual degree (B.Tech and M.Tech) biological engineering program of IIT Madras.
Title: Mechanisms that define regeneration vs. scarring.
Date/Time: 6.30 pm, 19th December 2020
Link: https://meet.google.com/fum-odmb-oas
Biography of the Speaker:
Srinivas Allanki graduated from the IIT Madras B.Tech. + M.Tech. Biotechnology dual degree program in 2016. He is now a final year Ph.D. student working with Dr. Sven Reischauer and Prof. Didier Stainier at the Max Planck Institute for Heart and Lung Research in Germany. Using the highly regenerative zebrafish as a model system, he studies the fundamental mechanistic differences between regeneration and forming a permanent and functionally inert scar after tissue damage.
Abstract:
The two diametrically opposed outcomes of tissue damage are fibrosis and scarring, or regeneration and functional repair. Species like zebrafish predominantly display a regenerative program resulting in the functional replacement of injured tissues, including the heart and appendages. Adult mammals predominantly activate a fibrotic program leading to the formation of a functionally inert scar. A key question remains as to how regenerative species escape an excessive fibrotic response. In this study, using combinatorial expression profiling and analyzing regeneration of multiple tissues in five mutants, we identify the first global upstream mechanism of regeneration in zebrafish. Moreover, using lineage tracing and human primary cell culture, we show that this mechanism prevents mammalian-like scarring in zebrafish. These observations open a novel entry point into the question as to why mammals react to tissue damage predominantly by fibrotic scarring over activating a regenerative program.
The Biotech Research Club is excited to host Dr. Aman Kumar, a post doctoral associate at the Goodman lab in the Yale School of Medicine. He obtained his PhD from UT Southwestern Medical Center in Molecular Microbiology in 2020 and his B.Tech in Biotechnology from IIT Madras in 2015.
Title: Interplay between tryptophan metabolites and the virulence factors of enteric pathogens
Date/Time: 7:15pm, 12th December 2020
Link: https://meet.google.com/syj-mbcy-zxq
Biography of the Speaker:
Dr. Aman Kumar graduated from IIT Madras in 2015 with a B.Tech + M.Tech in Biotechnology and went on to do a Ph.D. at the University of Texas Southwestern Medical Center, where he worked on host-pathogen-commensal interactions in the human gut in the lab of Prof. Vanessa Sperandio. He is currently a postdoctoral research associate in the lab of Prof. Andrew Goodman at the Yale School of Medicine.
Abstract:
Microbial establishment within the gastrointestinal (GI) tract requires surveillance of the gut biogeography. The gut microbiota coordinates behaviors by sensing host- or microbiota-derived signals. Here we show that the tryptophan derivatives including the microbiota-derived indole and the host-derived serotonin decreases the virulence of enteric pathogens. We utilized C. rodentium (a mouse-specific model pathogen) to understand the dynamics of host-pathogen-microbiome interactions and show that both indole and serotonin decrease the expression of virulence-related genes in C . rodentium. Mechanistically, we also identified the bacterial membrane bound histidine kinase CpxA as an indole and serotonin sensor. Taken together, our data indicate that bacterial pathogen senses the gut info-chemicals to establish a successful infection.
The Biotech Research Club is excited to host Ms. Nandita Damaraju, an alumnus of the 2014 batch of the B.Tech Biotechnology program from IIT Madras. She is currently a machine learning scientist at Inflammatix Inc., San Fransisco, USA.
Click on the image below to watch the recording!
Title: Data Science opportunities in Biotech
Date/Time: 9.30 pm, 8th December 2020
Link: https://meet.google.com/shv-bqzk-vwd
Biography of the Speaker:
Nandita Damaraju completed her bachelor’s degree in Biotechnology from IIT Madras in 2014. She is currently Machine Learning Scientist at Inflammatix, Inc. San Francisco, USA. She has previously also worked at Thermo Fisher Scientific as a Data Scientist. She holds a master’s degree in Computational Science and Engineering from Georgia Institute of Technology.
Abstract: Data science is being increasingly leveraged to solve many problems in the biotech industry. Within the Biotech industry, however, data science can mean many different things depending on the company or application. As a Machine Learning Scientist in the biotech industry, I want to talk about my experience navigating the plethora of opportunities available at this exciting interdisciplinary intersection, how data science in biotech differs from other industries, and the rich potential of avenues combining life and data science.
Biotech Research Club is hosting a talk by Jay Panji, a PhD scholar at Université Libre de Bruxelles in Brussels, Belgium. The talk will be followed by a general discussion session for students to interact with the speaker.
Title: Modeling the development and function of the blood-brain barrier in zebrafish.
Date/Time: 7PM, 21st November 2020
Venue: Google Meet
Link: http://meet.google.com/ket-pqsu-aum
Biography of the Speaker: Jay Panji is currently a first-year PhD candidate at the Université Libre de Bruxelles in Brussels, Belgium. His research interests lie in understanding the mechanisms involved in blood-brain barrier formation and how they are perturbed in neurodegenerative disorders. He is currently working on developing a zebrafish model of the blood-brain barrier.
Abstract: Blood vessels are more than passive conduits for blood flow. Tissue-specific vascular beds not only match the metabolic demands of the perfused organs but also act as important signalling centres releasing angiocrine factors that govern tissue morphogenesis and function. Proper brain function relies on elaborate neurovascular communications that, when perturbed, often have disabling or fatal consequences. Hence, there is great interest in studying the mechanisms that shape the anatomy and control the functionality of the cerebrovasculature, not only to better understand how the brain develops and works, but also to elaborate innovative therapeutic strategies for neurological disorders. Neurovascular biology is a relatively young field and an integrated model of how, when and to what extent neural and vascular development are coordinated is currently lacking. Building this model will greatly benefit from the combined capacity to (i) scrutinize the cellular modalities of the highly dynamic processes of neurovascular development in real-time and to (ii) identify experimental settings where the signalling and circulatory functions of the blood vessels can, at least partially, be uncoupled.
Biotech Research Club is hosting a talk by Dr. Kartik Gupta, a graduate student in the Cell and Molecular Biology program at the University of Wisconsin – Madison. The talk will be followed by a general discussion session for students to interact with the speaker.
Title: Helming Yama’s Buffalo: Molecular Regulation of RIPK3 Mediated Programmed Necrosis in Physiology and Disease
Date/Time: 7.30 PM, 6th November 2020
Venue: Google Meet
Link: https://meet.google.com/hmm-qujj-qrp
Biography of the Speaker: Kartik Gupta grew up in New Delhi and received a bachelor’s degree in Biotechnology from Amity University and was a summer research fellow in many institutes such as ICGEB, NII, JNU and AIIMS. Driven by the scientific curiosity that this training had instilled, he joined the MS (research) program at IIT-M and worked in Dr. Aradhyam Gopala Krishna’s lab from 2012-14 while spending one semester as part of DAAD scholarship at TU-Munich. He joined the Cell and Molecular Biology (CMB) graduate program at the University of Wisconsin– Madison in 2014 in the lab of Dr. Bo Liu where he studied the basic science aspects of cell death with relevance to cardiovascular diseases. Outside of the lab, he is a coffee aficionado and also enjoys weightlifting and running.
Abstract: Multiple programmed cell death (PCD) pathways have been discovered over the past 15 years that have challenged the synonymity of PCD with apoptosis. RIPK3 mediated programmed necrosis (or necroptosis) is unique within PCD pathways in its ability to proceed in the absence of caspases– proteases that are widely involved in apoptosis and other PCDs. Instead, necroptosis occurs via sequential post-translational modifications involving the RIP kinases RIPK1 and RIPK3. Although the factors involved in necroptosis differ from apoptosis, the signalling complexes involved in key decision-making steps are shared, and how cells choose one form of PCD over the other remains a fascinating area of investigation. In this talk, I provide an overview of various PCDs and how this decision-making process plays out in deciding apoptosis over necroptosis in the same cell. I present data from my own research arguing that the cellular abundance of RIPK3 (which is a bottleneck in necroptosis) is regulated via multiple transcriptional and post-translational mechanisms and is key in this decision-making process. I will also present some recent findings from our lab and others on how the necroptotic machinery moonlights with the endosomal pathway leading to extracellular vesicle biogenesis.
Biotech Research Club is hosting a talk by Dr. Siddhant Jain, a postdoctoral fellow at Harvard Medical School. The talk will be followed by a general discussion session for students to interact with the speaker.
Title: Dysregulation of Polycomb-mediated gene silencing in pediatric gliomas
Date/Time : 7.30 PM IST, 31st October, 2020
Biography of the Speaker: Siddhant Jain recently obtained his PhD from the Department of Biomolecular Chemistry at University of Wisconsin-Madison. He completed his B.Tech. in Biotechnology from IIT Roorkee. He is interested in understanding the enzymes that alter chromatin structure and regulate gene expression in eukaryotes. In his doctoral work in Dr. Peter Lewis’ lab, he discovered the biochemical function of a novel oncogene, EZHIP. He is off to a postdoctoral position with Dr. Cigall Kadoch at Harvard Medical School.
Abstract: An aberrant transcriptional profile is a hallmark of several cancers. Chemical modifications of DNA and histones, modulate chromatin structure and regulate transcription. Consequently, enzymes that catalyze addition or removal of these chemical modifications are frequently mutated in cancers. Recent studies have identified recurrent histone H3K27M mutations or aberrant expression of EZHIP in Diffuse Midline Gliomas and a subtype of ependymomas. In my doctoral studies, we characterized the biochemical function of these oncoproteins as competitive inhibitors of a chromatin-modifying enzyme – Polycomb Repressive Complex 2 (PRC2). I will discuss the molecular function of PRC2 and the mechanism by which these oncogenes drive highly aggressive pediatric gliomas.