2022 End-of-the-year summary!
Dear friends and colleagues, here we are at the end of 2022. Lots of things happened in all our lives, surely some good and some not so good. But here we are still, and we feel obliged to send a huge thank you to all our mentors, collaborators, funding support, engineers repairing our equipment, administration, and also those of you that (with just a few words or a smile) helped us with the challenges that science presents every day. In ways you cannot even imagine, you all supported the Sidoli lab to keep going and make great progress in our research program.
A few numbers to prove our record year. Our instruments processed nearly 5,000 samples this year, many of them from our 160 different collaborators (from 106 different labs). This year, we published 19 papers, of which two worth highlighting are our collective JoVE paper (link) and our first research article on spheroids (link). We also have 27 manuscripts currently in the peer-review process (link to CV page), so it will surely be a 2023 full of exciting news.
The lab is proud to remind you that Dejauwne, Ronnie and Sarah passed their Qual exam this year, and became PhD candidates! We have made great progress with our 3D cell models (link), the optimization of CRISPRi and locus-specific proteomics (link), our single-cell proteomics pipeline (link), the resolution of oxidation footprinting, the robustness of our high-throughput platform (including software for rapid signal extraction)... and we surely forgot many other important things. This year, we have created the world's first portable 3D cell incubator! That was crazy, CelVivo friends!
We are also very excited for all the interactions we had. We went to the Epigenetics Symposium in Philadelphia and met a lot of new friends; we absolutely rocked at the ASMS conference, including the presentation of 2 talks and 4 posters. We had a lot of nice people working in our lab this year: Elizabeth, Yukta, Zoe, and Laxmi (link). We also extend a special thank you to Giorgio Oliviero (University of Dublin, now Waters) to come virtually into our team for 6 long lectures and help us introduce DIA-based proteomics into our pipeline.
Thank you for working with, or simply be interested, in the Sidoli lab! We know life is not always kind but, if you are reading this, it is likely because you made an impact on ours. To a great 2023!
December 2022
Stephanie’s baby shower!
The lab publishes a paper in “Epigenetics & Chromatin” describing the use of 3D cell culture to study long-term inheritance in vitro. A special thank you to Stephanie, Ronnie, Jenny and Eddie for making this happen (link).
Interesting trivia: Simone makes it to the list of Top 2% world cited scientists for 2021, curated by Stanford University (link). Within this list, he is ranked in the top 32% in the category “Biochemistry & Molecular Biology”.
Simone comes back from the Eastern Analytical Symposium, where he received the Young Investigator Award. A special thank you to Ben Garcia (Washington University in St. Louis), who kindly agreed to Chair the session, as well as Kasia Kulej (The Children’s Hospital of Philadelphia) and Martin Wuhr (Princeton University) for participating to the symposium dedicated to the award. Below, an image of happy friends from the event.
Paperwork finalized for Laura Corveleyn (UGhent, Belgium) and Cassia Michael (Einstein)! They will join our lab early next year for an international exchange and lab rotation, respectively.
Congratulations to Ronnie and Simone, who will present a poster and a lightning talk at the next US HUPO in March 2022 in Chicago.
New shared grant alert: the "Era of Hope" from the Department of Defense has awarded a grant to the laboratory of Dr. Sam Bakhoums (Memorial Sloan Kettering), in which our lab will contribute with the proteomics analysis of mini-chromosomes.
Another collaborative grant! This time with Dr. Kartik Chandran (Einstein), who received an R21 from NIAID to study poxvirus.
New collaborative paper out in BioRxiv. Our collaborator Dr. Ian Maze describes another new histone modification related to neurobiology: "Histone monoaminylation dynamics are regulated by a single enzyme and promote neural rhythmicity" (link).
The lab hosts Dr. Richard Lauman (The Children’s Hospital of Philadelphia) for collaborating on a project using mass spectrometry to sequence tRNA and identify its modifications.
Below, an image from the Washington DC office of CelVivo. Anyone recognizes the people in the picture frame??
Simone chats with the Twitcher Benedict Aleh Ogadinma (Twitch account: “Mentediversa”) about ethics and mechanisms for genetic editing, and modifying organisms for lab use and general public (in Italian).
November 2022
We are happy to share a moving “Happy birthday” video dedicated to one of our closest collaborators, Dr. Matthew Scharff. Matty has been an incredible mentor for our group, and a critical collaborator for developing with us locus-specific proteomics enrichment (BioRxiv link). Please, enjoy the video below made by our friends at Einstein!
Congratulations to Stephanie for another great collaboration with the Morey lab (U Miami) published in Nature Structural & Molecular Biology (link)! Check out also the News & Views editorial about the paper (link).
If you missed Ronnie’s presentation at the Single Cell Proteomics Day symposium in Parma (Italy), check it out below!
October 2022
Congratulations to Ronnie for being selected as speaker at the Single Cell Proteomics Day symposium in Parma (Italy) on October 12th (link)!
A new paper in BioRxiv for Stephanie, this time a collaboration with the Peri Kurshan lab on neurobiology and C. elegans (link). Fingers crossed for a rapid publication!
Simone is assisting the setting up of a new start-up for -omics data analysis. The United States Patent and Trademark Office has published the protection of the mark “DeliverOmics”, the new name of the start-up (link). More info coming when its services will be available!
New collaborative paper: “Morphine disrupts macrophage functions even during HIV infection”, published in the Journal of Leukocyte Biology (link). Thank you to our collaborators, the Berman lab at Einstein!
September 2022
New preprint from the lab! Stephanie pioneered the use of spheroids cell culture to investigate chromatin memory (link). The manuscript is now under revision; fingers crossed!
We simplified the view of the “Funding and Awards” section, as it was starting to become quite confusing (link). We hope you will like more this new layout.
Congratulations to Yan who contributed to a publication of the Cuervo lab (Einstein) in press at Aging Cell (link).
A new collaborative paper with the Lengner and Hamilton labs (UPenn) titled “Autophagic state prospectively identifies facultative stem cells in the intestinal epithelium” is just published in EMBO Reports (link).
The Single Cell Proteomics symposium in Parma (Italy) is being finalized. Consider registering to attend virtually or in-person!
Our work on locus-specific proteomics to study how B-cells generate a variety of antibodies using DNA mutations of the immunoglobulin gene is online in BioRxiv (link). Fingers crossed for the paper that is in peer-review!
Congratulations to Dejauwne, Sarah and Ronnie for receiving their official certification for passing their Qual Exam. As of today, they officially hold a Master of Science! Now to the full PhD!
Simone will participate to the panel discussion “Transition to first independent position”. If you are interested in discussing some of the typical challenges of an academic career, or any related questions, feel free to register at this link (link).
August 2022
The lab says goodbye to Yukta and Zoe. Thank you for the great time during your summer volunteer work. It has been a real joy to work with both of you. You truly stood up to the task of working in a science lab, and showed great professionality. Best of luck for your last high school year!
New collaborative funding have been recently awarded! This means new very exciting projects coming our way (brief list below):
- Johanna Daily (Einstein) has been awarded an R01 titled “Defining the mechanism of coma in cerebral malaria”. We will work with her to analyze small molecules produced by our body in malaria patients that can potentially induce coma.
- Lluis Morey and Ramiro Verdun (University of Miami) have been awarded a co-PI R01 to investigate the role of the oncohistone H3K36M. We will help them by studying the proteins that interact with damaged chromatin in cells with this mutation.
- David Kass (Johns Hopkins) got a perfect score on his R35 renewal grant! We will help his group to study the cross-talk between metabolism and histone modifications in heart attack. A special thank you to Edwin, as he is the one bonding our two labs!
July 2022
Our JoVE protocol paper is online!! Thank you to the entire lab for the hard work. Awesome video! (link)
The IUBMB focused meeting on 'Integrative Omics of Nuclear Functions' has been successfully funded, so it will take place on October 15th to 19th 2023 in Chania/Greece. Mind-blowing speakers will present at the event; take a look at the calendar (link), and stay tuned for more info on registration!
The Single Cell Proteomics Symposium organized by the Italian Mass Spectrometry Society is officially open for registrations (in person or virtual). Consider joining, as you will hear also our work on single cell proteomics (link for registration).
The Eastern Analytical Symposium session honoring the work of the Sidoli lab has been finalized (image below). The event will be on November 15th in Plainsboro, New Jersey.
Simone will present on October 21st at the Chinese ASMS conference (link). Thank you very much to the organizing committee for the invitation!
Well done to Stephanie for a new collaboration with the Huangfu lab (MSKCC) uncovering a central requirement for HHEX in pancreatic lineage commitment and plasticity restriction (link).
June 2022
Welcome to the lab also to Xinyi (Zoe) Zhang! Our high school student cohort is complete. Lots of projects this summer!
Another collaboration is published in collaboration with the laboratory of Dr. Louis Weiss, Einstein (link). The project focuses on the mechanics and consequences of protein interactions of the intracellular parasite Toxoplasma gondii.
The lab welcomes Yukta Shah! Yukta is a high school student who will work with us as volunteer until the end of August.
A new collaboration on macrophage dysregulation by methamphetamine is published in Biomedicines (link).
The lab says goodbye to Elizabeth, who completed her rotation in the lab. Thank you for all your hard work in testing our portable incubator! We will put together a manuscript soon. Best of luck for your PhD in the lab of Dr. Louis Weiss; I know we will meet again soon!
Simone is interviewed by the magazine “Chemical & Engineering News” (C&EN) to discuss new discoveries and frontiers of the histone code science (link).
The lab comes back from an AMAZING experience at the ASMS annual conference! Edwin and Stephanie gave fantastic talks, where they received lots of questions and praises for their incredible work. Jenny, Sarah, Ronnie and Carlos presented their great science with posters, where they received many visits from curious colleagues. This was the very first ASMS attended as “Sidoli lab”, so it will be surely remembered. Thank you everyone for the great discussions and smiles. We will be back next year!
Photo album of the ASMS 2022 is available at this link.
May 2022
Great Slam for our students in passing the Qual exams!! Congratulations to Dejauwne, Ronnie and Sarah to become PhD candidates! Exciting future ahead!
Simone visits Chiesi Farmaceutici for strategizing the 2022 Single Cell symposium organized by IMaSS. Chiesi is one of the world’s most important pharma companies (2nd in Italy for revenue), of which headquarters are in Simone’s hometown (Parma, Italy).
Simone gives a lecture at the University of Parma on “How to analyze histone modifications, and why it is important”.
The EMBO course on protein modifications and cell signaling in Odense (Denmark) is finished! Simone helped with teaching about histone modifications, protein acetylation and proteomics data processing. Thank you everyone for the wonderful time!
Fortune Italia includes the bio of Simone on their “40 under 40” article (link).
Our newest JoVE paper on the analysis of histone modifications using 3D cell culture models is published online (link)! Congratulations to the entire lab for this community effort, and in particular to Jazmine for leading the work.
A new collaboration between the lab of Bridget Shafit-Zagardo (Einstein) and our lab is posted on BioRxiv (link). Thank you to Sarah for being the point of reference for the collaboration.
Congratulations to Jenny for her new collaboration with the Lalezari lab at Montefiore (link). The paper focuses on “Altered abundances of human immunoglobulin M and immunoglobulin G subclasses in Alzheimer’s disease frontal cortex”.
The ASMS agenda is out! Here are all the dates and places of our presentations (2 talks and 4 posters). You can click on the image to zoom in.
April 2022
The lab completes the recording of the protocol paper for the journal JoVE. The paper with video with be out soon!
The lab receives the Pilot & Feasibility Research Grant from the Einstein-Mount Sinai Diabetes Research Center (link)! Thank you for this generous support for our work, and congratulations to Edwin for leading the project that granted the award.
Simone is cited in the award page of the Eastern Analytical Symposium 2022 (link).
New collaboration investigating the role of the transcription factor PAX8 in ovarian cancer is out in Science Signaling (link).
Another collaborative paper for Yan, who is on fire lately! Here is an exciting study of the lab of Dr. Ira Tabas (Columbia University) investigating how macrophages use apoptotic cell-derived methionine and DNMT3A during efferocytosis to promote tissue resolution (link).
Simone joins the planning committee for the year 2022 of the Italian Society for Mass Spectrometry (IMaSS). To all the Italians and non-Italians around the world, consider joining our society (link)! It is obviously not as big as ASMS, but it is an exciting community rich of exchanges and talented scientists.
For the Einstein community, Simone will discuss how to negotiate a start-up package for faculty position on April 13th (link). For young students and postdocs interested in an academic career, we promise a plain-spoken type of meeting (not the usual obvious advice).
March 2022
Congratulations to Yan for the collaborative paper with the labs of Schramm and Tyler on a new inhibitor for the human DNA Methyltransferase 1 (link).
The Sidoli lab joins the initiative “Global Research Groups Supporting Ukrainian Scientists”. If you are a group leader with the possibility of supporting new scientists in the lab, and you are interested in the initiative, please leave your contact here (link).
Elizabeth Weyer joins the lab as new rotation student. Welcome to the team!
We will be well-represented this year at the ASMS in Minneapolis. Congratulations to Stephanie and Edwin for being accepted for an oral presentation, and to Carlos, Jenny, Ronnie and Sarah for being accepted for a poster presentation!
Some members of the lab participate to the Epigenetics Symposium in Philadelphia (link).
Simone is invited for a seminar at the Wistar Institute in Philadelphia. Thank you to Drs. Alessandro Gardini and Italo Tempera for organizing the visit.
First tests for the portable ClinoStar (image below)
February 2022
New old publication in collaboration with the labs of Xudong Wu, Ole N. Jensen and Kristian Helin (link). The project reveals that CpG island reconfiguration assists the polycomb repressive complex to promote exit from naive pluripotency. Interesting trivia: this is the new personal record for Simone in terms of data “longevity” (mass spec runs acquired in July 2011)!
The lab has a specific open position for a project investigating chromatin proteomics in longevity (link). Please, write us an email if interested!
Unfortunately, Laxmi is leaving us already. He got a great position at Regeneron (New York). Thank you for sharing the time you could with us, and all the best for the continuation of your career.
The lab hires an old friend, Dr. Giorgio Oliviero, for a 6-lecture course in the newest FragPipe and DIA-NN versions. Indeed, one of the best ways to stay up to date with proteomics when too many new things happen in our field. Highly recommended!
Simone gives a (virtual) lecture at the European School of Molecular Medicine in Milan, Italy (link) on data processing in proteomics.
The lab is selected in the Early Access Program for the NanoMosaic technology (link). Just a quick reminder that out there it is open war to mass spectrometry for how next-generation proteomics will be performed in the next decade!
The lab receives multiple visits from CelVivo this month to upgrade our ClinoStars, in particular to create the first beta version of portable 3D cell incubators.
We finally updated the section Alumni (link). The lab is still young, but we have had great people coming and going who are worth mentioning.
The Albert Einstein College of Medicine ranks #1 in New York City, #2 in New York State and #35 nationally in best midsize US employers according to Forbes (link).
Our collaboration with Dr. Johanna Daily on the role of pipecolic acid in cerebral malaria (link) is on the cover of The Journal of Infectious Diseases (link). Well done!
January 2022
Happy New Year! The lab starts slowly in 2022 due to restrictions, quarantines, little accidents and return from holidays. We will be back fully operative on Monday January 10th.
The lab welcomes Laxmi Narayan Mishra to the team!! Laxmi is a postdoc with a lot of experience in chromatin biology. Thank you for joining the lab!
First paper of 2022: great collaboration with the Shechter lab (Einstein) to investigate protein arginine methyltransferases and their ability to regulate post-transcriptional intron detention (link).
Congratulations to Yan and Stephanie for the great collaboration with the Chandran lab (Einstein): Genotype-specific features reduce the susceptibility of South American yellow fever virus strains to vaccine-induced antibodies (link).
The EMBO course in protein post-translational modifications is back on (link). Simone will be teaching histone proteomics. Fingers crossed that we will be able to do it in person and meet in the lovely Odense (Denmark)!
A second baby from the lab: congratulations to Laxmi and his wife Prasoon for expanding the family! Happy life to all of you!
One more collaboration with the lab of Ben Garcia (WashU in St. Louis): a remarkable effort in investigating the different biological role of a histone modification (H3K27me3) on different variants (canonical H3 vs H3.3) (link).
Simone is re-elected in the Senate Council of the Albert Einstein College of Medicine to represent the category of Assistant Professors.
A middle-down collaboration with the South African team of Dr. Lyn-Marie Birkholtz, investigating the dynamic changes of the histone code in the malaria parasite (link).
One more paper from a very productive January! An older project from the Berger and Garcia lab presents a controversial concept: histone acetylation on specific residues functions as reservoir for the cell when it needs to activate genes in absence of acetyl-CoA supply (link).