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WEAVER LAB

UT SOUTHWESTERN MEDICAL CENTER

DEPARTMENT of PHARMACOLOGY


PROTEOLYTIC MECHANISMS in CELL SIGNALING

Evidence across diverse phyla of metazoans depicts a new landscape for proteolytic factors, such as caspases, as not only effectors but key regulators of many cellular processes. In particular, genetic masking has hitherto limited our ability to observe many so-called "non-canonical" caspase functions that our work has recently brought to light. Now is an exciting time to be part of this rapidly emerging field.


The over-arching theme of the Weaver Lab is to deeply understand how proteolytic factors mediate diverse physiological functions.  Along those lines, we have identified CED-3 caspase working to support a variety of cellular functions ranging from limiting symmetric divisions of a stem-like cell type during cell fate decisions to opposing p38 MAPK stress signaling and downstream gene expression program to promote development. We find that caspases often work with other regulatory pathways to achieve their non-canonical functions.


Current lines of inquiry include: (1) how a given caspase is able to distinguish cell death from cell vigor substrates, (2) how proteolytic factors sculpt gene expression dynamics and (3) what upstream inputs license one proteolytic function over another. Unmasking these mechanisms is critical to understanding diverse disease processes including cancers and degenerative diseases.


To tackle these and other challenging questions, we employ a cross-disciplinary approach including genetics, proteomics, metabolomics and biophysical analyses. The Weaver lab utilizes C. elegans, mammalian cell culture, and biochemical models. Equipped with powerful tools, we are setting out to understand how proteolytic factors execute a potentially vast array of functions.

 

PEOPLE

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DR. BENJAMIN WEAVER

Principal Investigator

   

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DR. YI MIAO WEAVER

Sr. Research Scientist

Structure function studies of proteolytic factors

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DR. WANG YUAN

Post-Doctoral Researcher

Roles of caspases and p38 MAPK in development

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DR. HAI WEI

Post-Doctoral Researcher

Caspases in stress responses

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FRANCISCO CALVA MORENO

MSTP Graduate Student

Ph.D. Candidate

Center for Regenerative Science and Medicine Fellowship

UBR E3 ligases in development and disease

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IRVIN GARZA

DBS Graduate Student

Rotation Student

Neural Science Training Program Fellowship

Coming this Fall

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WE ARE STILL RECRUITING!!


Grad Student applicants: Apply through the umbrella program and send Ben an email.

Post-Doc and Technician applicants: email Ben with your letter of interest.

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2022 Aging Meeting

Madison WI

 

RESEARCH

Current Priorities and Training Environment

The Weaver lab is interdisciplinary and employs state of the art CRISPR mutagenesis, genetic, biochemical, proteomic, transcriptomic, metabolomic, and imaging methods to analyze dynamic processes in development, aging and stress responses. Using C elegans, mammalian cell culture, and in vitro models, our goal is to understand how proteolytic factors regulate critical cell signaling decisions. Understanding these mechanisms is crucial to diverse disease etiologies including cancers, degenerative diseases, and developmental disorders.  Our lab has exceptional facilities for advanced microscopy, cell culture, and  molecular biology. Trainees joining the Weaver lab will learn cutting-edge methodologies in diverse disciplines.  We have an array of ongoing studies with several areas of emphasis indicated below. Trainees will have distinct projects developed with substantial mentoring.

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CELL SIGNALING

We recently unmasked a broad array of genes working with caspase outside of cell death. Using proteomic, genetic, and cell biological approaches, we are probing the network and mechanisms of caspases in sculpting cell signaling.

GENE EXPRESSION DYNAMICS

We recently showed CED-3 caspase and PMK-1 p38 MAPK balancing stress-responsive and developmental functions. We are using a big data approach including genomics, proteomics, and translatomics to understand how broadly caspases and p38 MAPKs act in gene expression dynamics.

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CELL FATE

Using genetic, biochemical, and genomic approaches we demonstrated a non-canonical caspase function working in parallel to the miRISC pathway was critical to ensure temporal cell fate patterning limiting symmetric cell divisions at a critical developmental window. We are expanding these studies to understand the roles of proteolytic factors in mediating cell fate decisions.

STRESS RESPONSES

Throughout metazoans, caspases have been assoicated with stress responses. We recently showed how CED-3 caspase antagonizes activation of a pathogen response. We are using advanced CRISPR methods combined with omic approaches and advanced cell imaging to understand how developmental and stress-responsive states are dynamically regulated.

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DIFFERENTIAL REGULATION

Across nematodes, flies, and mammals, classic cell death caspases have been found with critical non-canonical functions supporting cell vigor.  We are using genetic and biochemical methods to understand how a given caspase with both cell death and cell vigor functions is differentially regulated.

SUBSTRATE RECOGNITION

We recently showed that the CED-3 caspase required a UBR-type E3 ubiquitin ligase to efficiently cleave and degrade LIN-28 in vivo. We further showed that the caspase and E3 ligase may form a complex. We are using biochemical and biophysical methods to understand how proteolytic factors recognize distinct substrates to achieve diverse functions.

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SELECTED PUBLICATIONS

2022

Balancing p38 MAPK Signaling with Proteostasis Mechanisms Supports Tissue Integrity during Aging in C. elegans

Yuan W, Weaver YM, Earnest S, Taylor CA, Cobb MH, Weaver BP bioRxiv July 12, 2022


​2020


Non-Canonical Caspase Activity Antagonizes p38 MAPK Stress-Priming Function to Support Development

​Weaver BP, Weaver YM, Omi S, Yuan W, Ewbank JE, Han M  Dev Cell 53(3):  358-369

Featured in Development or Disease: Caspases Balance Growth and Immunity in C. elegans

Olya Yarychkivska and Shai Shaham Dev Cell 53(3): 259-260

2018

Tag team: Roles of miRNAs and Proteolytic Regulators in Ensuring Robust Gene Expression Dynamics.

Weaver BP, Han M Trends Genet. 34(1):21-29   


2017

Coupled Caspase and N-End Rule Ligase Activities Allow Recognition and Degradation of Pluripotency Factor LIN-28 during Non-Apoptotic Development.

Weaver BP, Weaver YM, Mitani S, Han M Dev. Cell 41(6):665-673   

Featured in Partners in Crime

Barbara Conradt Dev Cell 41(6):  573-574

2016

Time to move the fat.

Weaver BP, Sewell AK, Han M Genes Dev. 30(13):1481-1482   

2014
CED-3 caspase acts with miRNAs to regulate non-apoptotic gene expression dynamics for robust development in C. elegans.

Weaver BP, Zabinsky R, Weaver YM, Lee ES, Xue D, Han M eLife e04265

Featured in Development: Cell Death Machinery Makes Life More Robust

Cristina Aguirre-Chen and Christopher M Hammell eLife 3:e05816

Also featured in For Caspases, An Escape from Death

Beverly A Purnell Science 347(6218): 142-143

 
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LAB NEWS

November 2022

Ben was honored to come back to his alma mater to give the "Alvin Sarachek Research Seminar" to the Department of Biological Sciences at Wichita State University!

September 2022

Francisco awarded fellowship from Hamon Center for Regenerative Science and Medicine!

​​July 2022

Wang's first author paper posted on bioRxiv

https://doi.org/10.1101/2022.07.12.499791

June 2022

Hai selected to give a talk at the Physiology retreat!

April 2022

Francisco selected to give a talk at the CMB graduate symposium!

April 2022

Weaver lab moved into its newly renovated space!

​​May 2021

Francisco passed his qualifying exams!

March 2021

Wang wins the Weaver Lab Spring Pretty Gel Competition!

​February 2020

Dr. Hai Wei joins the lab for post-doctoral studies!

November 2019

Francisco Calva Moreno joins the lab for graduate studies!

July 2019

Ben's MIRA grant funded through NIGMS!

May 2019

Dr. Wang Yuan joins the lab for post-doctoral studies!

April 2019

Ben's Welch Foundation grant funded!

September 2018

Weaver Lab established!

Ben and Yi get to work in the Department of Pharmacology at UT Southwestern Medical Center.

Post-Doc Years

Ben and Yi worked in Min Han's HHMI lab at CU Boulder where we discovered a non-canonical function for CED-3 caspase --along with other proteolytic factors--in cell fate determination. 

 

GALLERY

Worm Void
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Sometimes It Works
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Glow On!
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Choices, Choices
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Gel Biologists
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Flying By
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Stretching Out
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Phenotypical
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Small but Fast
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Making Mutants
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Cell Milieu
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Real Grinder
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Columns of Data
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Stacks and Stacks
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Happy PI
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Roundup
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Reckon So
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Plasticity
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FUN

Food for Thought

Not too surprisingly, biochemistry was born out of early efforts to perfect the enzymology and chemistry behind the fermentation of grains, fruits and milk to generate the varieties of dough, beer, wine and cheese that we know today from around the globe.  Here are a few glimpses of having some fun experimenting outside the lab.

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TRADITIONAL PIE of CHINA by HAI

Power-packed gems filled with pork and cabbage. Seasoned with salt, soy sauce, oil, garlic, ginger, and green onion.  Hai’s pro-tip:  Make the outside bun with fermented dough.  After lightly frying, pop these little party favorites into the oven for a crispy baked finish you won’t soon forget!

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BEEF RAMEN NOODLES by YI

Fusion of ramen noodles seasoned lightly with onion and parsley for a hearty combo.  Yi’s top-shelf ingredients…Tie this simple masterpiece together with Napa cabbage boiled in a soy-based broth. Add wood-smoked beef slices on top for a simple but super-delicious meal!

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FAJITAS by FRANCISCO

Visually stunning arrangement of fajitas served with guacamole, beans, pico de galla and rice. 

That’s not all!  Francisco threw in a loaf of baked banana bread for a super-satisfying finish!

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HOT POT by WANG

Traditional Chinese sensation that begins with a spicy soup stock and an assortment of meats, veggies, starchy noodles and you’re ready to roll!  Wang's philosophy:  best part is that you can add anything, this dish knows no limits!  What more could you ask for?

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NON-CANONICAL BARBECUE by BEN

Savory homemade marinades with thyme, cumin and bay leaf combined with hickory and cherry wood smoke for a decadent, savory flavor.  How to plate?   Ben likes to serve up his BBQ with grilled asparagus and homemade potato salad.

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Hai joins the lab, New Years 2020!!!

Sorry Wang and Francisco...

We forgot to take pictures of your celebrations.

Oops

 

CONTACT

​Interested in joining?  We would love to hear from you.

benjamin.weaver [at] utsouthwestern.edu

This website reflects only the views of the author and  is  not  a  publication  of  UT Southwestern,  which  bears  no responsibility for its content.


UT Southwestern Medical Center

Pharmacology

6001 Forest Park Rd

Dallas, TX 75390

USA

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