bioRxiv; group Benton

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Intersecting experimental evolution and CRISPR screens to identify novel toxin resistance loci

Michele Marconcini, Steeve Cruchet, Srishti Goswami, Raghuvir Viswanatha, Matthew Butnaru, Joydeep De, Camilla Roselli, Dafni Hadjieconomou, Norbert Perrimon, Stephanie E Mohr, Richard Benton

Abstract

Understanding toxin resistance in insects is key to appreciate niche adaptations but remains challenging due to its often-polygenic basis. A well-known example is the specialized association of Drosophila sechellia with noni fruit ( Morinda citrifolia ), which is toxic to most other insects, including the closely-related drosophilids D. simulans and D. melanogaster . Noni toxicity is due to its high concentration of octanoic acid (OA), but the mechanisms that determine sensitivity or resistance to OA remain poorly understood. Here, we experimentally-evolved D. simulans with increased OA resistance, identifying multiple loci under selection. Cross-referencing these with a genome-wide, OA-resistance CRISPR screen in a D. melanogaster cell line highlighted two proteins: Kraken, a putative detoxification enzyme expressed in digestive and renal tissues, and Alkbh7, a mitochondrial protein linked to fatty acid metabolism. Both genes show elevated expression in D. sechellia and OA-resistant D. simulans . In D. melanogaster , kraken mutants are more OA-sensitive, while Alkbh7 overexpression increased OA resistance. Importantly, mutation of these genes in D. sechellia reduced OA tolerance. Our identification of genes underlying OA resistance in laboratory and natural contexts demonstrates how complementary, cross-species selection approaches can provide insights into complex mechanisms of toxin susceptibility and adaptation, and have practical applications in the characterization of novel insecticides.

Cell.; co-auth. group van Leeuwen

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Global genetic interaction network of a human cell maps conserved principles and informs functional interpretation of gene co-essentiality profiles

Maximilian Billmann  1 , Michael Costanzo  2 , Xiang Zhang  3 , Arshia Z Hassan  3 , Mahfuzur Rahman  3 , Kevin R Brown  4 , Katherine S Chan  4 , Amy Hin Yan Tong  2 , Carles Pons  5 , Henry N Ward  6 , Catherine Ross  2 , Jolanda van Leeuwen  2 , Michael Aregger  2 , Keith A Lawson  7 , Barbara Mair  2 , Amy F Roth  8 , Nesli E Sen  9 , Duncan T Forster  7 , Guihong Tan  2 , Patricia Mero  4 , Sanna N Masud  10 , Yoonkyu Lee  6 , Magali Aguilera-Uribe  11 , Matej Ušaj  2 , Sylvia M T Almeida  7 , Kamaldeep Aulakh  4 , Urvi Bhojoo  7 , Saba Birkadze  11 , Nathaniel Budijono  3 , Xunhui Cai  12 , Joseph J Caumanns  2 , Jordan J Chalmers  11 , Megha Chandrashekhar  7 , Daniel Chang  3 , Ryan Climie  2 , Kuheli Dasgupta  11 , Adrian Drazic  13 , Jose I Rojas Echenique  2 , Rafael Gacesa  2 , Adrian Granda Farias  11 , Andrea Habsid  4 , Ira Horecka  7 , Kristin Kantautas  7 , Fenghu Ji  12 , Dae-Kyum Kim  14 , Seon Yong Lee  4 , Wendy Liang  2 , Hyobin Julianne Lim  7 , Kevin Lin  6 , Xueyibing Lu  3 , Michael Maier  15 , Babak Nami  4 , Allison Nixon  7 , Nicholas Mikolajewicz  4 , Milad Mokhtaridoost  4 , Lyudmila Nedyalkova  2 , Thomas Rohde  16 , Maria Sartori Rodrigues  2 , Martin Soste  2 , Eric Schultz  3 , Wen Wang  3 , Ashwin Seetharaman  2 , Ermira Shuteriqi  2 , Olga Sizova  4 , David Thomson Taylor  17 , Maria Tereshchenko  18 , David Tieu  7 , Jacob Turowec  2 , Tajinder Ubhi  19 , Sylvia Varland  13 , Kyle E Wang  7 , Zi Yang Wang  7 , Jiarun Wei  11 , Yu-Xi Xiao  11 , Philipp G Maass  11 , Bruno Reversade  15 , Grant W Brown  19 , Benjamin F Cravatt  20 , Scott J Dixon  21 , Haley D M Wyatt  18 , Hannes L Röst  2 , Frederick P Roth  22 , Tian Xia  23 , Gary D Bader  7 , Robbie Loewith  9 , Nicholas G Davis  8 , Brenda Andrews  24 , Chad L Myers  25 , Jason Moffat  26 , Charles Boone  27

Affiliations

Abstract

Deciphering how genes interact within human cells is essential for understanding their functional wiring and for developing targeted therapeutic strategies. In this study, we present a genome-scale map of genetic interactions in the human haploid cell line HAP1, based on CRISPR-based perturbation of ∼4 million gene pairs. The resulting network comprises ∼89,000 high-confidence gene-gene interactions, organizing genes into hierarchical modules corresponding to protein complexes and pathways, biological processes, and cellular compartments, mirroring principles observed in yeast and highlighting the functional architecture of a human cell. This large-scale genetic network complements the DepMap gene co-essentiality network by capturing unique functional information, uncovering roles of previously uncharacterized genes, and identifying molecular determinants of cancer-cell-line-specific genetic dependencies. This study presents a general data-driven strategy for systematically exploring the roles of genes and their functional connections in human cell lines.

Keywords: genetic interactions; genetic network conservation; genetic suppression; genome-scale genetic interaction network; genome-wide CRISPR screens; human haploid cells; synthetic lethality.

EMBO Rep.; co-auth. W. Wahli

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Hepatic FGF21 is not required for fasting metabolism but guides protein appetite post energy depletion

Justine Bruse  1 , Clothilde Marbach  1   2 , Arnaud Polizzi  1 , Tatiana Landre  3 , Juliette Salvi  3 , Valérie Alquier-Bacquie  1 , Shiou-Ping Chen  4 , Marine Huillet  1 , Clémence Rives  1 , Céline M P Martin  1 , Prunelle Perrier  1 , Fadila Benhamed  5 , Marion Régnier  5 , Stefan Weger  6 , Claire Naylies  1 , Yannick Lippi  1 , Caroline Sommer  1 , Mikael Albin  1 , Frédéric Lasserre  1 , Thierry Levade  7   8 , Michael Schupp  9 , Laurence Gamet-Payrastre  1 , Léon Kautz  10 , Nicolas Loiseau  1 , Walter Wahli  1   11 , Sandrine Ellero-Simatos  1 , Céline Cruciani-Guglielmacci  4 , Alexandra Montagner  12 , Alexandre Benani  3 , Catherine Postic  5 , Hervé Guillou #  13 , Anne Fougerat #  14

Affiliations

Free article

Abstract

Fasting initiates a coordinated metabolic response to preserve energy balance. As glycogen stores are depleted, the body transitions to mobilizing fatty acids from adipose tissue and generating ketone bodies in the liver to sustain the function of vital organs. A network of hormonal signals and transcriptional programs coordinate these adaptations. Among these, the hepatokine fibroblast growth factor 21 (FGF21) is strongly upregulated during fasting and has been proposed as a key mediator of the fasting response. To investigate the physiological functions of FGF21, we study mice with hepatocyte-specific deletion of Fgf21. Although the liver is the primary source of circulating FGF21 during fasting, its absence in hepatocytes does not alter typical fasting-induced gene expression or key metabolic pathways such as hepatic gluconeogenesis, adipose tissue lipolysis, or ketone production. Instead, we uncover a distinct role for FGF21 in promoting protein appetite following a fast. These findings challenge the conventional view of hepatocyte-produced FGF21 as a fasting-acting hormone and reveal a more specialized function in guiding nutrient selection after energy depletion.

Time to change your PCR end-of-run from 4°C to 12°C? The GTF already has.

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A simple protocol tweak that, for routine applications, preserves sample quality, protects your instrument and reduces unnecessary energy use.

CIG’s Genomics Technology Facility (GTF) has already switched. It uses a 12°C final hold for a wide variety of library preparation workflows (RNAseq, WGS, single cell libraries…) with no observed impact on data quality after sequencing.

The 4°C end-of-run hole is set by default in many labs, but it is unnecessary in most routine applications. PCR products are far more stable at ambient temperatures than is often assumed, and any residual Taq Polymerase activity at 12°C may only be a concern in a small number of sensitive downstream applications, not for standard workflows.

Maintaining 4°C often harms more than it helps. Prolonged cold holds keep Peltier modules under sustained load, accelerating wear on a component that is costly to replace. Very low temperatures also increase the risk of condensation inside the instrument, which can promote corrosion and electronic failures over time. Finally, maintaining 4°C is among the most energy-demanding states of a thermocycler, drawing energy unnecessarily.

What to do
  • Set your final hold to 12°C. This is sufficient for standard retrieval time windows, including overnight runs – collect your tubes the following morning without concern.
  • Check whether your protocol has specific requirements. Some applications do (e.g. blunt-end cloning workflows). If in coubt, contact roberto.sermier@unil.ch at the GTF before adjusting your settings.
  • See it for yourself. Run a quick side-by-side at 4°C vs 12°C on your own samples. For a routine PCR, band quality and yield will tell you everything you need to know.

FURTHER READING

Tip of the Month -PCR hold-V3Download

Science Ethics at CIG, 6th Edition, May 28, 2026

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Research integrity is not just about extreme misconduct — it is also about the human biases that insidiously push science from responsible practice toward questionable habits, undermining reproducibility and credibility.

This seminar offers concrete tools and strategies applicable at the bench and largely relevant to any researcher, whatever their field—including if you attended last year, as content has been updated.

In this year’s keynote lecture, Joe Garner (Stanford University) proposes a powerful mindset shift in experimental design illustrated by examples from animal research, but broadly applicable beyond the animal lab: moving from “what did we control?” to “what did we choose to ignore — and at what cost?”.

When, where

  • Date : Thursday May 28, 1:00–4 :45 PM
  • Location : Geopolis, room 1612 (UNIL Mouline)
  • Followed by an apéritif

Who should attend?

  • Compulsory for CIG PhD students and postdocs who joined since March 21, 2025.
  • 0.5 day RESAL credit for continuing education in Animal Experimentation: register
  • All welcome —250 participants last year, from across the Lemanic area.

Programme

Introduction : Research integrity – The Good, the Bad and the Ugly — Frédéric Preitner

Ethics at the bench (1): Managing bias in experimental design and data visualization — Frédéric Schutz

Ethics at the bench (2): Beautification, manipulation, and AI: ethics of scientific images — Romain-Daniel Gosselin

The FBM Ombudsman introduces himself —Christian Kern

Keynote lecture : Changing the scientific mindset in biomedical studies — Joe Garner (Stanford University)

About the keynote speaker

Joe Garner is Professor of Comparative Biomedicine at Stanford University, where his work on animal models and experimental design has made him one of the leading voices on reproducibility in biomedical research. His keynote challenges researchers to move beyond “what did we control?” and ask instead: “what did we choose to ignore — and at what cost?”

Further information about Joe Garner’s work

Beyond3Rs: https://med.stanford.edu/beyond3rs.html
Stanford website: med.stanford.edu/profiles/Joseph_Garner
Papers: scholar.google.com/citations?user=JThS8LMAAAAJ
Mouse ethogram: www.mousebehavior.org

Talk abstracts

  1. Keynote lecture: Changing the scientific mindset in biomedical studies (Joe Garner). This seminar explores a necessary shift in perspective in biomedical research: moving from the question “What have we controlled for?” to a more critical one: “What have we chosen to ignore, and at what cost?” Using examples from studies employing animal models, it highlights six common blind spots that can compromise scientific conclusions: ignored differences in the biology of the animal model, ignored characteristics of the modeled human disease, ignored limitations of the measurements used, ignored environmental factors, ignored impacts of animal welfare, and ignored principles of experimental design and statistics. The seminar demonstrates how recognizing these implicit assumptions can improve the validity, reproducibility, and ethical foundations of biomedical research.
  2. Ethics at the bench (1): Experimental design and data presentation (Frédéric Schutz). This seminar examines sources of bias in research, with examples from mouse studies. It shows how bias can arise even when researchers act in good faith, and why safeguards such as controls, randomization, and blinding are essential. It also emphasizes that the goal of science is not to prove hypotheses but to challenge them rigorously. The seminar further explores how uncontrolled environmental variability—such as cage effects, where animals sharing a cage are not statistically independent—can influence experimental outcomes. Finally, it addresses bias in data visualization and reporting, highlighting how misleading graphs or ambiguous error bars can distort interpretation and emphasizing the need for transparent presentation of data.
  3. Ethics at the bench (2): Beautification, manipulation, and AI: ethics of scientific images (Romain Gosselin). This seminar examines ethical issues related to the handling and manipulation of scientific images in biomedical research, mostly focusing on immunoblotting. It emphasizes that digital images are full-fledged data that must be handled with the same rigor as any other dataset. The presentation discusses how choices made during image acquisition, processing, analysis, and reporting can introduce bias. It also reviews common questionable practices, such as excessive contrast adjustment, saturation, cropping, or duplication of image elements. Finally, the seminar highlights the concerns raised by the abrupt rise of generative artificial intelligence, which now enable the generation of highly realistic synthetic images indiscernible from genuine images. Implications for research integrity and the need for awareness, good practices, and appropriate detection tools are discussed.
  4. Presentation of the FBM Ombudsman (Christian Kern). The Ombudsman of the Faculty of Biology and Medicine (FBM) at UNIL will introduce his role and mission. He will explain the mechanisms for reporting suspected scientific misconduct, which may arise in all types of research—clinical or basic—and may involve human subjects, animals, or biological material. In cases of suspected misconduct, the Ombudsman acts as an advisory and guidance authority. The Ombudsman will present several examples of situations that may constitute breaches of scientific integrity in clinical practice or laboratory research.