RIVERHEAD, N.Y. - A Long Island architect was charged Friday with murder in the deaths of three of the 11 victims in a long-unsolved string of killings known as the Gilgo Beach murders after detectives pursuing a new lead say they matched DNA from a pizza he ate to genetic material found on the women’s remains.

Rex Heuermann, who has lived for decades across a bay from where the remains were found, is charged with killing Melissa Barthelemy, Megan Waterman and Amber Costello. He is also considered the prime suspect in the death of a fourth woman whose body was bound and hidden in thick underbrush along a remote beach highway, authorities said.

Heuermann, 59, was arrested late Thursday amid a renewed investigation that tied him to a pickup truck a witness reported seeing when one of the victims disappeared in 2010. In March, detectives tailing Heuermann recovered his DNA from pizza crust in a box that he’d discarded in a Manhattan trash can and matched it to DNA from a hair found on a restraint used in the killings, authorities said.

Heuermann’s lawyer entered a not guilty plea on his behalf Friday in state court in Riverhead. Judge Richard Ambro ordered him jailed without bail, citing “the extreme depravity” of his alleged conduct.

Heuermann’s lawyer, Michael Brown, said they’d just learned about the charges Friday morning. Speaking to reporters after the arraignment, he said Heuermann told him: “I didn’t do this.”

Heuermann, wearing khaki pants and a gray collared shirt, did not speak in court.

Heuermann lives in Massapequa Park, a community just north of South Oyster Bay and the sandy stretch known as Gilgo Beach where skeletal remains were found along a remote oceanfront highway in 2010 and 2011. Most of the victims were young women who had been sex workers. Their deaths long stumped investigators, a mystery that fueled immense public attention and led to a 2020 Netflix film, “Lost Girls.”

Determining who killed them, and why, has vexed a slew of seasoned homicide detectives through several changes in police leadership. Last year, an interagency task force was formed with investigators from the FBI, as well as state and local police departments, aimed at solving the case.

After linking Heuermann to the pickup truck, prosecutors said investigators were able to connect him to other evidence, including the burner cellphones used to arrange meetings with the slain women, and taunting calls that a person claiming to be the killer made to one of Barthelemy’s relatives using her cellphone after she disappeared in 2009.

In recent months, Heuermann sought to keep tabs on the probe and “searched obsessively” on the internet for facts about the Gilgo Beach killings, including the names of women he’s accused of killing, as well as podcasts and documentaries about the case, Suffolk County District Attorney Ray Tierney said.

Tierney said authorities moved to charge Heuermann now with three of the killings “out of concern for this defendant fleeing and the danger to the community.” They are continuing to work toward charging him in the death of a fourth Gilgo victim, Maureen Brainard-Barnes.

Until his arrest, Heuermann continued to use burner phones, patronize sex workers and search the internet for sadistic materials, including sexually exploitive images of children, Tierney said. He also has access to 92 handguns, the prosecutor said.