PRESS-NEWS.org - Press Release Distribution
PRESS RELEASES DISTRIBUTION

FunMap reveals a functional network of genes and proteins in human cancer

2024-12-11
(Press-News.org) Large-scale protein and gene profiling have massively expanded the landscape of cancer-associated proteins and gene mutations, but it has been difficult to discern whether they play an active role in the disease or are innocent bystanders. In a study published in Nature Cancer, researchers at Baylor College of Medicine revealed a powerful and unbiased machine learning-based approach called FunMap for assessing the role of cancer-associated mutations and understudied proteins, with broad implications for advancing cancer biology and informing therapeutic strategies.

“Gaining functional information on the genes and proteins associated with cancer is an important step toward better understanding the disease and identifying potential therapeutic targets,” said corresponding author Dr. Bing Zhang, professor of molecular and human genetics and part of the Lester and Sue Smith Breast Center at Baylor.

“Our approach to gain functional insights into these genes and proteins involved using machine learning to develop a network mapping their functional relationships,” said Zhang, member of Baylor’s Dan L Duncan Comprehensive Cancer Center and a McNair Scholar. “It's like, I may not know anything about you, but if I know your LinkedIn connections, I can infer what you do.”

The team developed FunMap, a functional network of 10,525 genes constructed using a supervised machine learning method that integrates protein datasets and RNA sequencing data from 11 cancer types recently harmonized by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) pan-cancer working group.

“With FunMap, we found 196,800 associations among 10,525 proteins – a comprehensive and unbiased proteomic coverage and a high level of functional relevance,” Zhang said. “Two key differences between our approach and previous gene co-expression network studies are first, the integration of cancer protein data with mRNA expression data and second, the application of supervised machine learning to synergize all datasets to maximize the predictive power. Unexpectedly, our approach outperformed protein–protein interaction networks in discriminating between functionally relevant and irrelevant gene pairs.”

Through network analysis, FunMap uncovers protein modules and a hierarchical modular organization linked to cancer hallmarks and clinical characteristics, predicts the functions of understudied cancer proteins, offers deeper insights into established cancer drivers and identifies drivers with low mutation frequency.

“More than 200 genes are highly overexpressed or under-expressed in cancer, but we know very little about their specific roles in the disease,” Zhang said. “When we mapped these genes in our network, we were able to look at the neighborhood and make a prediction about their function.”

For example, the expression of the understudied gene MAB21L4 is significantly below normal in three types of cancer tumors. FunMap showed that this gene’s network neighborhood is enriched for genes associated with epithelial cell differentiation, the suppression of which plays a critical role in tumor progression. Clinical tumor grading data, together with a recent study showing that loss of MAB21L4 blocks differentiation to drive the development of squamous cell carcinoma, provide strong evidence to support a tumor suppressor role of MAB21L4.

Moreover, leveraging cutting edge deep learning methods with FunMap uncovered numerous previously unrecognized cancer drivers with low mutation frequencies, including a novel tumor suppressor role for LGI3, supported by gene knockout experimental data.  

This study highlights the great potential of integrating machine learning and proteogenomic profiling to gain a deeper understanding of complex cancer systems. By generating a comprehensive functional network, this approach provides a robust framework for cancer functional genomics research, offering valuable insights into mutations and cancer-associated proteins.

“These findings can greatly aid in prioritizing targets for clinical translation, ultimately contributing to the development of more effective cancer therapies,” Zhang said.

The FunMap Python package is fully open source and available for download from the Python Package Index (https://pypi.org/project/funmap).

Co-first authors, Zhiao Shi and Jonathan T. Lei, and John M. Elizarraras, also contributed to this work. All are affiliated with Baylor College of Medicine.

The authors acknowledge contributions from the CPTAC and its Pan-Cancer Analysis working group. This work was supported by National Institutes of Health grants from the National Cancer Institute (U24 CA210954, U24 CA271076, R01 CA245903 and U01 CA271247), by the Cancer Prevention and Research Institute of Texas (CPRIT) (award RR160027), a CPRIT scholarship and a cancer scholarship by the McNair Medical Institute at the Robert and Janice McNair Foundation.

###

END


ELSE PRESS RELEASES FROM THIS DATE:

First full characterization of kidney microbiome unlocks potential to prevent kidney stones

2024-12-11
Cleveland Clinic researchers have found definitive proof of a kidney microbiome that influences renal health and kidney stone formation, demonstrating that the urinary tract is not sterile and low levels of bacteria are normal. The Nature Communications publication describes the rigorous multi-pronged approach a team led by Aaron Miller, PhD, and José Agudelo, MD, used to identify and characterize the small bacterial community by combining preclinical, human and dish studies.  They also identified certain bacteria within the microbiome ...

IMDEA Software researchers present MixBuy, a protocol for secure and privacy-preserving digital purchases

2024-12-11
IMDEA Software Institute researchers Diego Castejón Molina, Dimitris Vasilopoulos and Pedro Moreno-Sanchez present a system that represents a step forward in digital purchases. Their research is reflected in the study: “MixBuy: Contingent Payment in the Presence of Coin Mixers” which has been accepted at the Privacy Enhancing Technologies Symposium (PETS). Context Today, many products can be purchased with cryptocurrencies such as Bitcoin: video games, books or cell phone plans. In some countries, such as El Salvador, you can even buy ...

Having a good breakfast reduces cardiovascular risk

2024-12-11
Having a quality breakfast that provides the right amount of energy to face the day, around a quarter of daily intake, reduces the risk of cardiovascular disease. This is highlighted by a study conducted by the Hospital del Mar Research Institute and published in the Journal of Nutrition, Health and Aging. The study followed the progress of 383 participants in the PREDIMED-Plus project, a randomized clinical trial comparing the effects of a Mediterranean diet combined with physical activity versus dietary recommendations alone on cardiovascular disease. No previous study had analyzed the impact of energy intake and the nutritional ...

New study reveals provincial and territorial inequities and inadequacies in access to medications and treatment for cardiovascular conditions in Canada

New study reveals provincial and territorial inequities and inadequacies in access to medications and treatment for cardiovascular conditions in Canada
2024-12-11
A new study assessing provincial and territorial variations in reimbursement criteria of drug coverage for patients covered by Canada's public pharmacare programs for two common cardiovascular conditions revealed significant inequities and deficiencies in access to medications and treatment. The article appearing in the Canadian Journal of Cardiology, published by Elsevier, exposes the complexities of the Canadian drug review process and makes a case for a unified framework to improve the present infrastructure, moving towards ensuring the best care for patients with cardiovascular disease.   Canada has been praised for its universal healthcare system and low ...

Pre-seed funding to recolor the world greener

Pre-seed funding to recolor the world greener
2024-12-11
To commercialize a completely new way of creating colors, a coalition between Kobe University and the venture capital firm ANRI received startup development funding of ¥300 million from the Japan Science and Technology Agency (JST). With their lightweight, unfading and environmentally friendly way of producing color, they want to first enter the security ink and cosmetics markets before moving om to paints for cars, airplanes and other mobility applications. We color our world, and ourselves, to display information, to protect the underlying surface, to uniquely identify an object, ...

New research unlocks jaw-dropping evolution of lizards and snakes

New research unlocks jaw-dropping evolution of lizards and snakes
2024-12-11
A groundbreaking University of Bristol study has shed light on how lizards and snakes -the most diverse group of land vertebrates with nearly 12,000 species - have evolved remarkably varied jaw shapes, driving their extraordinary ecological success. This research, led by a team of evolutionary biologists and published in the Proceedings of the Royal Society B today, offers a new understanding of the intricate factors influencing the evolution of lower jaw morphology in these animals, known collectively as lepidosaurs. The researchers discovered that jaw shape evolution in lepidosaurs is influenced by a complex interplay of factors beyond ecology, ...

Cardiorespiratory fitness linked to preservation of cognitive abilities in older age

2024-12-11
Higher cardiorespiratory fitness in older age is linked to the preservation of several core aspects of cognitive ability that are vulnerable to age-related decline, finds research published online in the British Journal of Sports Medicine. And this association holds true irrespective of key risk factors for cognitive decline: age and carriage of the high risk APOE4 gene, the findings show.  Cardiorespiratory fitness is a physiological measure of aerobic capacity that can be modified by regular ...

Around 1 in 5 of the world’s under 50s living with genital herpes (HSV)

2024-12-11
Around 1 in 5 of the world’s under 50s—846 million people—are living with genital herpes infection, suggest the latest global estimates, published online in the journal Sexually Transmitted Infections.   And more than 200 million 15-49 year olds probably had at least one symptomatic outbreak of the infection in 2020, the latest year for which figures are available, the data analysis suggests. The findings prompt the researchers to call for the development of new treatments and vaccines ...

Cutting early life exposure to parental smoking may lower MS risk in genetically prone

2024-12-11
Cutting early life exposure to parental smoking may lower the risk of developing MS (multiple sclerosis) in those who are genetically predisposed to the disease, finds research published online in the Journal of Neurology Neurosurgery & Psychiatry. The interplay of genes and environmental factors, including smoking, alter key aspects of brain structure in early childhood, likely facilitating development of the disease and suggesting that there may be a window of opportunity to stave this off, conclude the researchers. MS is an autoimmune disease that is typically diagnosed between the ages of 20 and 40. But ...

High-flow nasal oxygen vs noninvasive ventilation in patients with acute respiratory failure

2024-12-11
About The Study: Compared with noninvasive ventilation, high-flow nasal oxygen met prespecified criteria for noninferiority for the primary outcome of endotracheal intubation or death within 7 days in 4 of the 5 patient groups with acute respiratory failure. However, the small sample sizes in some patient groups and the sensitivity of the findings to the choice of analysis model suggests the need for further study in patients with chronic obstructive pulmonary disease, immunocompromised patients, and patients with acute cardiogenic pulmonary edema. Corresponding Author: To ...

LAST 30 PRESS RELEASES:

Major review highlights latest evidence on real-time test for blood – clotting in childbirth emergencies

Inspired by bacteria’s defense strategies

Research spotlight: Combination therapy shows promise for overcoming treatment resistance in glioblastoma

University of Houston co-leads $25 million NIH-funded grant to study the delay of nearsightedness in children

NRG Oncology PREDICT-RT study completes patient accrual, tests individualized concurrent therapy and radiation for high-risk prostate cancer

Taking aim at nearsightedness in kids before it’s diagnosed

With no prior training, dogs can infer how similar types of toys work, even when they don’t look alike

Three deadliest risk factors of a common liver disease identified in new study

Dogs can extend word meanings to new objects based on function, not appearance

Palaeontology: South American amber deposit ‘abuzz’ with ancient insects

Oral microbes linked to increased risk of pancreatic cancer

Soccer heading does most damage to brain area critical for cognition

US faces rising death toll from wildfire smoke, study finds

Scenario projections of COVID-19 burden in the US, 2024-2025

Disparities by race and ethnicity in percutaneous coronary intervention

Glioblastoma cells “unstick” from their neighbors to become more deadly

Oral bacterial and fungal microbiome and subsequent risk for pancreatic cancer

New light on toxicity of Bluefin tuna

Menopause drug reduces hot flashes by more than 70%, international clinical trial finds

FGF21 muscle hormone associated with slow ALS progression and extended survival

Hitting the right note: The healing power of music therapy in the cardiac ICU

Cardiovascular disease risk rises in Mexico, despite improved cholesterol control

Flexible optical touch sensor simultaneously pinpoints pressure strength and location

Achalasia diagnosis simplified to AI plus X-ray

PolyU scholars pioneer smart and sustainable personal cooling technologies to address global extreme heat

NIH grant aims for childhood vaccine against HIV

Menstrual cycle and long COVID: A relation confirmed

WMO report on global water resources: 2024 was characterized by both extreme drought and intense rainfall

New findings explain how a mutation in a cancer-related gen causes pulmonary fibrosis

Thermal trigger

[Press-News.org] FunMap reveals a functional network of genes and proteins in human cancer