Evidence map›Paper›PMID 40505656›Full record

ArticleCell2025

Phenotypic landscape of an invasive fungal pathogen reveals its unique biology.

Michael J Boucher, Sanjita Banerjee, Meenakshi B Joshi, Angela L Wei, Matthew J Nalley, Manning Y Huang, Susan Lei, Massimiliano Ciranni, Andrew Condon, Andreas Langen and 12 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.

0numbers the graph read from it
0cells of the map it votes in
14citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

14 citing papers in PubMed.

  1. Article
  2. Article
  3. Copper Radical Oxidases Contribute to Virulence inPathogens (Basel, Switzerland) · 2026
    Article
  4. Article
  5. Article
  6. Article
  7. Article
  8. Article
  9. bioRxiv : the preprint server for biology · 2025
    Article
  10. Article
  11. Article
  12. Article
  13. Article
  14. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

22 authors.

Michael J BoucherDepartment of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
Sanjita BanerjeeDepartment of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
Meenakshi B JoshiDepartment of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
Angela L WeiDepartment of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
Matthew J NalleyDepartment of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
Manning Y HuangDepartment of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
Susan LeiDepartment of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
Massimiliano CiranniDepartment of Informatics, Bioengineering, Robotics and Systems Engineering, University of Genoa, 16145 Genoa, Italy.
Andrew CondonDepartment of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
Andreas LangenDepartment of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
Thomas D GoddardDepartment of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
Ippolito CaradonnaDepartment of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
Alexi I GoranovDepartment of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
Christina M HomerDepartment of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
Yasaman MortensenDepartment of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
Sarah PetnicDepartment of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
Morgann C ReillyDepartment of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
Yi XiongDepartment of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
Katherine J SusaDepartment of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
Vito Paolo PastoreDepartment of Informatics, Bioengineering, Robotics and Systems Engineering, University of Genoa, 16145 Genoa, Italy.
Balyn W ZaroDepartment of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
Hiten D MadhaniDepartment of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA. Electronic address: hitenmadhani@gmail.com.

Funding

MUTIDISCIPLINARY TRAINING PROGRAM IN LUNG DISEASEST32HL007185 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI David J Erle, LAURENCE HUANG · 1985 to 2026
$24.6M
Rapid production of SARS-CoV-2 molecular clones using CRISPR-based yeast recombineeringR01AI100272 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI MADHANI, HITEN D · 2012 to 2025
$11.3M
Microbial Pathogenesis and Host DefenseT32AI060537 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Joanne N. Engel · 2004 to 2026
$6.5M
Exploiting a high-precision phenotypic map to illuminate environmental sensing by a fungal meningitis pathogenR01AI187603 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Hiten D Madhani · 2025 to 2026
$1.2M
Illumina NovaSeq 6000 Sequencing SystemS10OD028511 · OD · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI CHOW, ERIC D · 2020 to 2020
$583k
Mechanisms of immune evasion by a neuroinvasive fungal pathogenF32AI152270 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI BOUCHER, MICHAEL JOSEPH · 2021 to 2023
$185k
NHLBI NIH HHS T32 HL007185NIAID NIH HHS F32 AI152270NIAID NIH HHS R01 AI100272NIAID NIH HHS R01 AI187603NIAID NIH HHS T32 AI060537NIH HHS S10 OD028511
6 · The paper itself

Abstract

Cryptococcus neoformans is the most common cause of fungal meningitis and the top-ranking WHO fungal priority pathogen. Only distantly related to model fungi, C. neoformans is also a powerful experimental system for exploring conserved eukaryotic mechanisms lost from specialist model yeast lineages. To decipher its biology globally, we constructed 4,328 gene deletions and measured-with exceptional precision-the fitness of each mutant under 141 diverse growth-limiting in vitro conditions and during murine infection. We defined functional modules by clustering genes based on their phenotypic signatures. In-depth studies leveraged these data in two ways. First, we defined and investigated new components of key signaling pathways, which revealed metazoan-like cellular machinery not present in model yeasts. Second, we identified environmental adaptation mechanisms repurposed to promote mammalian virulence by C. neoformans, which lacks a known animal reservoir. Our work provides an unprecedented resource for deciphering a deadly human pathogen.

Indexed as

Cryptococcus neoformansAnimalsCryptococcosisFemaleFungal ProteinsGene DeletionHumansMicePhenotypeSignal TransductionVirulenceFungal Proteins

Identifiers

PMID40505656
PMCPMC12407185

What OpenQuestion holds

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.