About

Kyle Cunningham is a Professor in the Department of Biology at Johns Hopkins University. His research focuses on understanding the molecular mechanisms governing drug resistance and virulence in pathogenic yeasts, particularly Candida glabrata. Cunningham's laboratory has developed innovative approaches, such as adapting Tn-seq (transposon mutagenesis coupled to next-generation DNA sequencing), to perform genome-wide screens that identify genes mediating antifungal resistance, colonization, invasion, survival within immune cells, and virulence in hosts. His work aims to elucidate how C. glabrata acquired its pathogenic capabilities and resistance traits, which are significant given the increasing incidence of infections and resistance in clinical settings. Cunningham's background includes a PhD from UCLA, postdoctoral training in mitochondrial membrane biogenesis at the University of Basel, and yeast genetics at the Whitehead Institute at MIT. He rejoined Johns Hopkins as an assistant professor in 1994 and has since contributed extensively to the understanding of fungal pathogenesis and resistance mechanisms.

Research topics

• Biology
• Computational biology
• Genetics
• Biochemistry
• Botany
• Cell biology
• Microbiology

Selected publications

• Expression of two forms of the calcium/calmodulin-dependent protein kinase Cmk2 is differentially regulated in response to calcium stress in budding yeast

  Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · 2025-11-23

  articleSenior author
  PublisherDOI

• Management of plaque protrusion in transcarotid artery revascularization with stent-in-stent technique

  Journal of Vascular Surgery Cases and Innovative Techniques · 2025-01-16

  articleOpen access

  Transcarotid artery revascularization (TCAR) has emerged as a promising alternative to carotid endarterectomy as an intervention for high risk carotid artery stenosis patients. TCAR provides superior neuroprotection as compared with transfemoral carotid stenting, as well as similar outcomes to carotid endarterectomy. Plaque prolapse (PP) through the stent while rare poses a significant risk of ischemic complications during TCAR. The patient presented with a left internal carotid artery stenosis that was inaccessible surgically. During TCAR, angiography revealed PP through the stent. A second stent was deployed with excellent results. This case highlights TCAR's advantage in managing PP with flow reversal. TCAR's enhanced neuroprotection offers a valuable option for addressing this complication, providing benefits that may not be fully achieved with transfemoral carotid stenting.

  PublisherDOI

• 39. Bacterial membrane vesicles and their interactions with macrophages and glial cells: alterations caused by the alcohol microbiota

  Alcohol · 2024-12-01

  article
  PublisherDOI

• Dedicated Chest Wall Injury Program quality review: How to create and incorporate a quality and safety program for surgical stabilization of rib fractures

  The Journal of Trauma: Injury, Infection, and Critical Care · 2024-09-27

  article

  BACKGROUND: Adoption of surgical stabilization of rib fractures (SSRF) in chest trauma necessitates outcomes reviews and process improvement (PI). As volume and complexity increase, such vigilance is imperative. Over 10 years, our center has developed a dedicated PI program based on our trauma PI program. Here, we outline the components of this program, aiming to share best practices and potentially improve SSRF patient outcomes. METHODS: Over 10 years, our dedicated SSRF PI process has evolved to include bimonthly reviews on case and quality metrics. In 2022, all patients at our single high-volume Level 1 trauma center with flail chest segments were identified, and a PI chart review was conducted. Data collected included management approach (operative vs. nonoperative), postoperative complications, mortality, patient demographics, trauma specific variables (Injury Severity Score, etc.), and rib fracture details. Operative data collected included number of ribs plated, system used, and complication rates for each surgeon and plating system used. RESULTS: Of 82 patients identified, 88% underwent SSRF. Among these, 49% experienced one or more postoperative complications, not all directly related to SSRF procedures. Mortality rate for SSRF patients was 15%, predominantly in those with Injury Severity Score of >25 and mean age of 58 years. Patients who had trauma activations and required emergency department chest tube placement had higher complications. The mean number of ribs stabilized was four. Complications occurred more frequently with posterior fractures. Outcomes were collated and analyzed at SSRF Outcomes Committee. CONCLUSION: The utilization of SSRF underscores the need for a rigorous quality review process to enhance patient safety and SSRF-specific outcomes. Our program developed over time from and was implemented in fashion similar to the trauma PI processes. The resulting quality initiative has fostered center-specific PI projects and programmatic advancements. LEVEL OF EVIDENCE: Economic and Value-Base Evaluations; Level IV.

  PublisherDOI

• Tn-seq of the <i>Candida glabrata</i> reference strain CBS138 reveals epigenetic plasticity, structural variation, and intrinsic mechanisms of resistance to micafungin

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-05-03 · 1 citations

  preprintOpen accessSenior authorCorresponding

  ABSTRACT C. glabrata is an opportunistic pathogen that can resist common antifungals and rapidly acquire multidrug resistance. A large amount of genetic variation exists between isolates, which complicates generalizations. Portable Tn-seq methods can efficiently provide genome-wide information on strain differences and genetic mechanisms. Using the Hermes transposon, the CBS138 reference strain and a commonly studied derivative termed 2001 were subjected to Tn-seq in control conditions and after exposure to varying doses of the clinical antifungal micafungin. The approach revealed large differences between these strains, including a 131 kb tandem duplication and a variety of fitness differences. Additionally, both strains exhibited up to 1000-fold increased transposon accessibility in subtelomeric regions relative to the BG2 strain, indicative of open subtelomeric chromatin in these isolates and large epigenetic variation within the species. Unexpectedly, the Pdr1 transcription factor conferred resistance to micafungin through targets other than CDR1 . Other micafungin resistance pathways were also revealed including mannosyltransferase activity and biosynthesis of the lipid precursor sphingosine, the drugging of which by SDZ 90-215 or myriocin enhanced the potency of micafungin in vitro . These findings provide insights into complexity of the C. glabrata species as well as strategies for improving antifungal efficacy. Summary Candida glabrata is an emerging pathogen with large genetic diversity and genome plasticity. The type strain CBS138 and a laboratory derivative were mutagenized with the Hermes transposon and profiled using Tn-seq. Numerous genes that regulate innate and acquired resistance to an important clinical antifungal were uncovered, including a pleiotropic drug resistance gene (PDR1) and a duplication of part of one chromosome. Compounds that target PDR1 and other genes may augment the potency of existing antifungals.

  PublisherOA PDFDOI

• Redefining Pleiotropic Drug Resistance in a Pathogenic Yeast: Pdr1 Functions as a Sensor of Cellular Stresses in <i>Candida glabrata</i>

  bioRxiv (Cold Spring Harbor Laboratory) · 2023-05-09 · 2 citations

  preprintOpen accessSenior authorCorresponding

  Abstract Candida glabrata is a prominent opportunistic fungal pathogen of humans. The increasing incidence of C. glabrata infections is attributed to both innate and acquired resistance to antifungals. Previous studies suggest the transcription factor Pdr1 and several target genes encoding ABC transporters are critical elements of pleiotropic defense against azoles and other antifungals. This study utilizes Hermes transposon insertion profiling to investigate Pdr1-independent and Pdr1-dependent mechanisms that alter susceptibility to the frontline antifungal fluconazole. Several new genes were found to alter fluconazole susceptibility independent of Pdr1 ( CYB5 , SSK1 , SSK2 , HOG1 , TRP1 ). A bZIP transcription repressor of mitochondrial function ( CIN5 ) positively regulated Pdr1 while hundreds of genes encoding mitochondrial proteins were confirmed as negative regulators of Pdr1. The antibiotic oligomycin activated Pdr1 and antagonized fluconazole efficacy likely by interfering with mitochondrial processes in C. glabrata . Unexpectedly, disruption of many 60S ribosomal proteins also activated Pdr1, thus mimicking the effects of the mRNA translation inhibitors. Cycloheximide failed to fully activate Pdr1 in a cycloheximide-resistant Rpl28-Q38E mutant. Similarly, fluconazole failed to fully activate Pdr1 in a strain expressing a low-affinity variant of Erg11. Fluconazole activated Pdr1 with very slow kinetics that correlated with the delayed onset of cellular stress. These findings are inconsistent with the idea that Pdr1 directly senses xenobiotics and support an alternative hypothesis where Pdr1 senses cellular stresses that arise only after engagement of xenobiotics with their targets. Importance Candida glabrata is an opportunistic pathogenic yeast that causes discomfort and death. Its incidence has been increasing because of natural defenses to our common antifungal medications. This study explores the entire genome for impacts on resistance to fluconazole. We find several new and unexpected genes can impact susceptibility to fluconazole. Several antibiotics can also alter the efficacy of fluconazole. Most importantly, we find that Pdr1 – a key determinant of fluconazole resistance – is not regulated directly through binding of fluconazole and instead is regulated indirectly by sensing the cellular stresses caused by fluconazole blockage of sterol biosynthesis. This new understanding of drug resistance mechanisms could improve the outcomes of current antifungals and accelerate the development of novel therapeutics.

  PublisherOA PDFDOI

• Usefulness of the Updated Brain Injury Guidelines for the Triage of Minimal Traumatic Brain Injury within a Trauma System

  Journal of the American College of Surgeons · 2022-10-14

  articleSenior author

  INTRODUCTION: Traumatic brain injuries (TBI) are associated with significant resource use. Select minimal TBI can potentially be treated in lower-acuity settings with fewer resources. The Updated Brain Injury Guidelines (UBIG) criteria (2018) were developed to guide resource use including hospital transfers. Our study examined the usefulness of UBIG to determine appropriate triage of minimal TBI within a regional trauma system. METHODS: A trauma system registry was queried (American College of Surgeons–verified Level I trauma center and 2 verified Level III trauma centers) for adult patients (18 years or older) with an AIS-Head score greater than 0. Penetrating injuries were excluded. The study period was 2020 to 2021. The primary outcome was mortality. Secondary outcomes included progression on imaging, neurosurgical intervention, clinical deterioration, and length of stay (Table). UBIG was compared to Injury Severity Score via generalized linear models as a benchmark for predictivity capability. Statistical analysis was performed with R version 4.0.5. Table. - Validation of Updated Brain Injury Guidelines (UBIG) Results Variable UBIG1 (n = 93) UBIG2 (n = 235) UBIG3 (n = 193) p Value Age (mean, y) 53.4 ± 21.2) 61.1 ± 20.5 64.9 ± 21 <0.0001 Sex (% male) 56 (60.9%) 142 (60.4%) 111 (57.5) 0.7906 Hospital length of stay (d) 3.9 ± 4.7 4.43 ± 7.2 8.2 ± 10.6) <0.0001 Worsening subsequent imaging 1 (1.1%) 14 (6%) 26 (13.5%) 0.0004 Clinical worsening 4 (4.4%) 23 (9.8%) 46 (23.8%) <0.0001 Neurosurgical intervention 0 (0%) 7 (3%) 43 (22.3) <0.0001 Mortality 1 (1.1%) 5 (2.1%) 15 (7.8%) 0.0039 Mortality odds ratio (95% CI) ref 1.9 (0.3–37.3) 7.5 (1.5–136.7) Clinical worsening odds ratio (95% CI) ref 2.4 (0.9–8.3) 6.9 (2.7–23.4) RESULTS: A total of 521 patients were identified (93 UBIG1, 235 UBIG2, 193 UBIG3). There was a significant difference between UBIG groups for outcomes of mortality, age, length of stay, worsening imaging, clinical deterioration, and neurosurgical intervention (all p < 0.05). For study outcomes, UBIG sensitivity was 63% to 86%, specificity was 68% to 71%, and AUC was 0.67 to 0.78. An extended model incorporating demographic variables demonstrated improved sensitivity (86%) and specificity (78%) with AUC of 0.86. CONCLUSION: UBIG classification can be safely applied to the triage of trauma patients presenting with TBI. Increasing UBIG status is associated with worse outcomes. Mild TBI patients with UBIG1 without other significant injuries are appropriate for management at Level III trauma centers. Our predictive model incorporating UBIG with age, sex, ethnicity, and race suggested improved accuracy compared with the UBIG alone.

  PublisherDOI

• Yeast cell death pathway requiring AP-3 vesicle trafficking leads to vacuole/lysosome membrane permeabilization

  Cell Reports · 2022 · 29 citations

  • Cell biology
  • Biology
  • Biochemistry

  Unicellular eukaryotes have been suggested as undergoing self-inflicted destruction. However, molecular details are sparse compared with the mechanisms of programmed/regulated cell death known for human cells and animal models. Here, we report a molecular cell death pathway in Saccharomyces cerevisiae leading to vacuole/lysosome membrane permeabilization. Following a transient cell death stimulus, yeast cells die slowly over several hours, consistent with an ongoing molecular dying process. A genome-wide screen for death-promoting factors identified all subunits of the AP-3 complex, a vesicle trafficking adapter known to transport and install newly synthesized proteins on the vacuole/lysosome membrane. To promote cell death, AP-3 requires its Arf1-GTPase-dependent vesicle trafficking function and the kinase Yck3, which is selectively transported to the vacuole membrane by AP-3. Video microscopy revealed a sequence of events where vacuole permeability precedes the loss of plasma membrane integrity. AP-3-dependent death appears to be conserved in the human pathogenic yeast Cryptococcus neoformans.

  PublisherOA PDFDOI

• 1301: INCIDENCE, OUTCOMES, AND RISK FACTORS OF POST-INTUBATION HYPOTENSION IN TRAUMA PATIENTS

  Critical Care Medicine · 2022-12-15 · 1 citations

  article

  Introduction: Cardiovascular deterioration is a recognized complication of emergency intubation. Post-intubation hypotension (PIH) has not been investigated in acute trauma resuscitation. We aim to identify the incidence, risk factors, and outcomes associated with PIH in emergency trauma resuscitation. Methods: Retrospective cohort study of emergency intubations performed from 2020 through October 2021 at Carolinas Medical Center. Data were extracted via the trauma database and manual chart review using a single reviewer and standard data collection instrument. Enrolled patients were 18 year or older, involved in trauma, and intubated in the Emergency Department. Patients with hypotension defined by systolic blood pressure < 90 mmHg, use of vasopressors, or cardiac arrest prior to intubation were excluded. PIH was defined as SBP less than 90 mmHg within 30 minutes if intubation. Patients with PIH were compared to those who did not experience PIH. Results: We identified 540 patients in our trauma database; 294 patients met criteria for the study. The mean patient age was 43 years old and 77.6% of patients were male. PIH occurred in 36 of 294 (12.2%) patients. Patients experiencing PIH did not have statistically higher mortality; 22.2% versus 15.9% (difference of 6.3%; 95% CI:-0.19 to 0.07; p = 0.34), but they did experience longer ICU length of stay: 8 versus 5.6 days (difference of 2.4 days; 95% CI: -4.23 to -0.46; p = 0.015) and longer hospital length of stay: 25.4 versus 12.3 days (difference of 13.1 days; 95% CI: -23.58 to -2.67; p = 0.01). PIH patients had higher pre-intubation shock index (0.8 versus 0.69, p < 0.01), had lower pre-intubation systolic blood pressure (133 mmHg versus 144 mmHg, p = 0.036), experienced higher number of intubation attempts (1.26 versus 1.07, p < 0.01), and were more likely to be female (0.56 versus 0.18, p = < 0.01). We invested comorbidities and medications associated with PIH and found that PIH patients had higher exposure to angiotensin converting enzyme (ACE) inhibitors at 17% compared to 3%; p < 0.01. Conclusions: PIH is a common complication of emergency intubation in trauma patients and is associated with higher complexity of illness as identified by ICU and hospital length of stay. We identified several clinical risk factors associated with PIH in trauma patients.

  PublisherDOI

• Gene-dependent yeast cell death pathway requires AP-3 vesicle trafficking leading to vacuole membrane permeabilization

  bioRxiv (Cold Spring Harbor Laboratory) · 2021-08-03 · 2 citations

  preprintOpen access

  Abstract Unicellular eukaryotes are suggested to undergo self-inflicted destruction. However, molecular details are sparse by comparison to the mechanisms of cell death known for human cells and animal models. Here we report a molecular pathway in Saccharomyces cerevisiae leading to vacuole/lysosome membrane permeabilization and cell death. Following exposure to heat-ramp conditions, a model of environmental stress, we observed that yeast cell death occurs over several hours, suggesting an ongoing molecular dying process. A genome-wide screen for death-promoting factors identified all subunits of the AP-3 adaptor complex. AP-3 promotes stress-induced cell death through its Arf1-GTPase-dependent vesicle trafficking function, which is required to transport and install proteins on the vacuole/lysosome membrane, including a death-promoting protein kinase Yck3. Time-lapse microscopy revealed a sequence of events where AP-3-dependent vacuole permeability occurs hours before the loss of plasma membrane integrity. An AP-3-dependent cell death pathway appears to be conserved in the human pathogen Cryptococcus neoformans .

  PublisherOA PDFDOI

Recent grants

• NIH Grant R21NS074072

  NIH · $158k · 2013

• NIH Grant R01GM053082

  NIH · $3.6M · 2009

• Functional genomics using auxin-inducible deletion analyses (AIDA)

  NIH · $434k · 2014–2018

• Identifying and characterizing a H+/Ca2+ exchanger that supports lactation

  NIH · $429k · 2014–2018

• NIH Grant R21NS057023

  NIH · $162k · 2007

Frequent coauthors

• Gerald R. Fink

  Whitehead Institute for Biomedical Research

  20 shared

• Zhengchang Su

  University of North Carolina at Charlotte

  16 shared

• Richard B. Marchase

  16 shared

• J. Edwin Blalock

  16 shared

• Feng Liang

  Wenzhou Medical University

  16 shared

• Jeffrey F. Harper

  University of Nevada, Reno

  16 shared

• Heven Sze

  University of Maryland, College Park

  16 shared

• Andrej Bugrim

  12 shared