Coscia Lab

The quantitative analysis of proteins in space and time, the building blocks of life that dictate health and disease, is key to our molecular understanding of severe diseases, such as cancer. Tumors are comprised of multiple cell types and phenotypic cellular states, which are often spatially organized in the complex tissue microenvironment. Studying these diverse cell types and their dynamic interplay on a global, quantitative and unbiased scale, requires novel multimodal concepts on the basis of interdisciplinary, translational research.

Our translational research group develops and applies mass spectrometry (MS) based proteomics workflows for spatially-resolved systems biology. For this purpose, we use a combination of analytical tools including multi-level proteomics (expression-, interaction- phospho-proteomics) and functional cell biology assays.

CosciaLab_2023 — From left to right: Fabian Coscia, Di Qin, Sonja Fritzsche, Jeannine Engel, Melissa Klingeberg, Janett König, Jose Nimo, Anuar Makhmut

We have recently co-developed Deep Visual Proteomics, a first-of-its-kind concept that combines high-resolution imaging, AI-guided image analysis and ultra-sensitive MS-based proteomics. Applied to preclinical models and archived biobank specimens, this concept allows us to gain unprecedented insights into cellular proteome heterogeneity.

Deep Visual Proteomics workflow illustration — © Coscia Lab, MDC

As part of the Berlin-centered Research Node ‘MSTARS’ (Multimodal clinical mass spectrometry to target treatment resistance), our MDC group closely collaborates with the Berlin Institute of Health, the Max Planck Institute for Molecular Genetics and the Humboldt University and the CHARITÉ. MSTARS, which is funded by the German Ministry of Science and Technology (BMBF) combines a broad range of complementary proteomic, metabolomic and imaging-based technologies with computational approaches for next-level patient care.

Our long-term vision is to decipher molecular and cellular disease pattern that can be used as predictive measures in precision oncology.

Melissa Klingeberg

Melissa.Klingeberg@mdc-berlin.de

Anuar Makhmut

Anuar.Makhmut@mdc-berlin.de

José Antonio Nimo Cabrera

Jose.Nimo@mdc-berlin.de

Di Qin

Di.Qin@mdc-berlin.de

Graduate and Undergraduate

Minh Tien Trinh

MinhTien.Trinh@mdc-berlin.de

May 03, 2024 / Br J Cancer

AHRR and SFRP2 in primary versus recurrent high-grade serous ovarian carcinoma and their prognostic implication

N. Monjé
M.P. Dragomir
B.V. Sinn
I. Hoffmann
A. Makhmut
T. Simon
C.A. Kunze
J. Ihlow
W.D. Schmitt
J. Pohl
I. Piwonski
S. Marchenko
C. Keunecke
T.G. Calina
F. Tiso
H. Kulbe
C. Kreuzinger
D. Cacsire Castillo-Tong
J. Sehouli
E.I. Braicu
C. Denkert
S. Darb-Esfahani
K. Kübler
D. Capper
F. Coscia
M. Morkel
D. Horst
C. Sers
E.T. Taube

March 20, 2024 / Mol Cell Proteomics

An automated and fast sample preparation workflow for laser microdissection guided ultrasensitive proteomics

A. Makhmut
D. Qin
D. Hartlmayr
A. Seth
F. Coscia

February 13, 2024 / EMBO Rep

The NSP3 protein of SARS-CoV-2 binds fragile X mental retardation proteins to disrupt UBAP2L interactions

D.H. Garvanska
R.E. Alvarado
F.O. Mundt
R. Lindqvist
J.K. Duel
F. Coscia
E. Nilsson
K. Lokugamage
B.A. Johnson
J.A. Plante
D.R. Morris
M.N. Vu
L.K. Estes
A.M. McLeland
J. Walker
P.A. Crocquet-Valdes
B.L. Mendez
K.S. Plante
D.H. Walker
M.B. Weisser
A.K. Överby
M. Mann
V.D. Menachery
J. Nilsson

November 15, 2023 / Cell Syst

A framework for ultra-low-input spatial tissue proteomics

A. Makhmut
D. Qin
S. Fritzsche
J. Nimo
J. König
F. Coscia

July 19, 2023 / Cell Syst

What do you most hope spatial molecular profiling will help us understand? Part 2

I. Yanai
E.J. Fertig
M. Li
F. Coscia
J. Klughammer
Q. Nie
J. Chen
A.F. Coskun

July 01, 2023 / Gastroenterology

Proteomic profiling of colorectal adenomas identifies a predictive risk signature for development of metachronous advanced colorectal neoplasia

J.M. Bech
T. Terkelsen
A.S. Bartels
F. Coscia
S. Doll
S. Zhao
Z. Zhang
N. Brünner
J. Lindebjerg
G.I. Madsen
X. Fang
M. Mann
J.M.A. Moreira

September 15, 2022 / Mol Cel

The TRESLIN-MTBP complex couples completion of DNA replication with S/G2 transition

G. Zonderland
R. Vanzo
S. Amitash
E. Martín-Doncel
F. Coscia
A. Mund
M. Lerdrup
J. Benada
D. Boos
L. Toledo

August 01, 2022 / Nat Biotechnol

Deep Visual Proteomics defines single-cell identity and heterogeneity

A. Mund
F. Coscia
A. Kriston
R. Hollandi
F. Kovács
A.D. Brunner
E. Migh
L. Schweizer
A. Santos
M. Bzorek
S. Naimy
L.M. Rahbek-Gjerdrum
B. Dyring-Andersen
J. Bulkescher
C. Lukas
M.A. Eckert
E. Lengyel
C. Gnann
E. Lundberg
P. Horvath
M. Mann

July 01, 2022 / Nat Neurosci

Identification of early neurodegenerative pathways in progressive multiple sclerosis

M. Kaufmann
A.L. Schaupp
R. Sun
F. Coscia
C.A. Dendrou
A. Cortes
G. Kaur
H.G. Evans
A. Mollbrink
J.F. Navarro
J.K. Sonner
C. Mayer
G.C. DeLuca
J. Lundeberg
P.M. Matthews
K.E. Attfield
M.A. Friese
M. Mann
L. Fugger

May 22, 2022 / Nat Biotechnol

A knowledge graph to interpret clinical proteomics data

A. Santos
A.R. Colaço
A.B. Nielsen
L. Niu
M. Strauss
P.E. Geyer
F. Coscia
N.J.W. Albrechtsen
F. Mundt
L.J. Jensen
M. Mann

Arbeitsgruppenleiter Fabian Coscia prüft die Proben

Press Release No. 39 September 05, 2023 Berlin

ERC Starting Grant awarded to Fabian Coscia

Whether aggressive cancer cells can spread unchecked depends, to no small degree, on their cellular neighborhood. Fabian Coscia wants to analyze exactly what happens at the proteome level during this interaction. He has now been selected for a €1 million-plus grant from the European Research Council (ERC) to pursue this research.

Science March 17, 2023

The key to the right treatment

Berlin-based research project MSTARS is entering its second round. Matthias Selbach and Fabian Coscia explain how the Max Delbrück Center is contributing, why the collaboration with Charité is so important, and how studying proteins in cells can help identify the best therapy for a patient.

Probenaufnahme in den Autosampler für LC-MS basierte Proteomik

Press Release No. 23 May 19, 2022 Berlin

Creating protein maps of tumors

A technique called Deep Visual Proteomics helps shed new light on cancer cell properties, a German-Danish team now reports in “Nature Biotechnology”. Fabian Coscia co-developed the new method and will further refine it at the MDC – with the aim of finding therapies for even resistant tumors.

Science July 08, 2021

📺 Fabian Coscia seeks to shed new light on cancer cells

Fabian Coscia is the head of the junior research group on Spatial Proteomics at the MDC. He uses artificial intelligence to analyze cancer cell proteomes – the entirety of the proteins produced by the cells. Now, he wants to develop this method further as part of the MSTARS project.

March 2024: Our second paper is out in Molecular & Cellular Proteomics!: We pioneered a robotic workflow for spatial tissue proteomics sample preparation based on the cellenONE. Congrats Anuar and Di for this shared success!
More info here: https://www.mcponline.org/article/S1535-9476(24)00040-9/fulltext

March 2024: Big welcome to Rafael, who just started his postdoctoral work!

Oct 2023: Our lab's first publication is out in Cell Systems!
Highlights•Detailed protocol and guidelines for ultra-low-input spatial tissue proteomics•Single-cell MS-based proteomics data obtained from archival FFPE tissue•MS signal allows to normalize across tissue types and sample amounts•Cytokines and transcriptional regulators quantified in tonsil microregionsMore info here: https://www.cell.com/cell-systems/fulltext/S2405-4712(23)00287-9

Sept 2023: Our lab was awarded an ERC Starting Grant!!!
Please see more info about the project here: https://www.mdc-berlin.de/de/news/press/erc-starting-grant-fuer-fabian-… (English)and here: https://cms2.mdc-berlin.net/de/news/press/erc-starting-grant-fuer-fabia… (German)

Aug 2023: What an achievement for Anuar winning the best short talk award at the Single-Cell Proteomics Conference in Vienna!

Congratulations Anuar!

July 2023: Melissa was awarded the MDC PhD fellowship!

Congrats to Melissa Klingberg, who did her Master's thesis in our lab. She was now awarded a PhD fellowship position for the International PhD Program at the Max Delbrück Center! Congrats Melissa, we are very happy to have you in our group!

May 2023: Our lab's first preprint is online! :-)

Congrats to the entire team and our first author Anuar. We describe a scalable workflow for ultra-low input FFPE tissue proteomics. Our microscopy-guided proteomics approach shows that single-cell analysis from FFPE tissue is principally achievable! A great basis for many biomedical applications in the near future.